Development of EST-based SSR and SNP markers in Gastrodia elata (herbal medicine) by sequencing, de novo assembly and annotation of the transcriptome

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dc.authorid0000-0002-7470-0080en_US
dc.authorid0000-0002-0595-5661en_US
dc.authorid0000-0001-5579-5179en_US
dc.contributor.authorWang, Yunsheng
dc.contributor.authorShahid, Muhammad Qasim
dc.contributor.authorGhouri, Fozia
dc.contributor.authorErcişli, Sezai
dc.contributor.authorBaloch, Faheem Shehzad
dc.date.accessioned2021-06-23T19:51:14Z
dc.date.available2021-06-23T19:51:14Z
dc.date.issued2019
dc.departmentBAİBÜ, Ziraat Fakültesi, Tarla Bitkileri Bölümüen_US
dc.description.abstractTianma (Gastrodia elata Blume) has unique biological characteristics and high medicinal value. The wild resource of G. elata is being overutilized and should be conserved as it is already included in the list of endangered species in China. The population size of cultivated G. elata is small because of domestication bottleneck. Therefore, it is of utmost importance to evolve high-quality varieties and conserve wild resources of G. elata. In this study, we sequenced tuber transcriptomes of three major cultivated sub-species of Gastrodia elata, namely G. elata BI. f. elata, G. elata Bl. f. glauca S. Chow, and G. elata Bl. f. Viridis, and obtained about 7.8G clean data. The assembled high-quality reads of three sub-species were clustered into 56,884 unigenes. Of these, 31,224 (54.89%), 25,733 (45.24%), 22,629 (39.78%), and 11,856 (20.84%) unigenes were annotated by Nr, Swiss-Port, Eukaryotic Ortholog Groups (KOG), and Kyoto Encyclopedia of Genes and Genomes (KEGG) databases, respectively. Here, a total of 3766 EST-SSRs and 128,921 SNPs were identified from the unigenes. The results not only offer huge number of genes that were responsible for the growth, development, and metabolism of bioactive components, but also a large number of molecular markers were detected for future studies on the conservation genetics and molecular breeding of G. elata.en_US
dc.identifier.doi10.1007/s13205-019-1823-4
dc.identifier.issn2190-572X
dc.identifier.issn2190-5738
dc.identifier.issue8en_US
dc.identifier.pmid31321198en_US
dc.identifier.scopus2-s2.0-85068795591en_US
dc.identifier.scopusqualityQ2en_US
dc.identifier.urihttps://doi.org/10.1007/s13205-019-1823-4
dc.identifier.urihttps://hdl.handle.net/20.500.12491/9950
dc.identifier.volume9en_US
dc.identifier.wosWOS:000474345100001en_US
dc.identifier.wosqualityQ3en_US
dc.indekslendigikaynakWeb of Scienceen_US
dc.indekslendigikaynakScopusen_US
dc.indekslendigikaynakPubMeden_US
dc.institutionauthorBaloch, Faheem Shehzad
dc.language.isoenen_US
dc.publisherSpringer Heidelbergen_US
dc.relation.ispartof3 Biotechen_US
dc.relation.publicationcategoryMakale - Uluslararası Hakemli Dergi - Kurum Öğretim Elemanıen_US
dc.rightsinfo:eu-repo/semantics/openAccessen_US
dc.subjectTraditional Chinese Medicineen_US
dc.subjectTianma (Gastrodia Elata Blume)en_US
dc.subjectNeuronen_US
dc.subjectSNPen_US
dc.subjectSSRen_US
dc.titleDevelopment of EST-based SSR and SNP markers in Gastrodia elata (herbal medicine) by sequencing, de novo assembly and annotation of the transcriptomeen_US
dc.typeArticleen_US

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