Open AccessMining of simple sequence repeats (SSRs) loci and development of novel transferability-across EST-SSR markers from de novo transcriptome assembly of Angelica dahurica
Author(s) -
Chen Chen,
Youjun Chen,
Huang Wen-juan,
Yuansheng Jiang,
Huihui Zhang,
Wei Wu
Publication year - 2019
Publication title -
plos one
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 0.99
H-Index - 332
ISSN - 1932-6203
DOI - 10.1371/journal.pone.0221040
Subject(s) - transferability , microsatellite , biology , transcriptome , computational biology , genetics , expressed sequence tag , sequence assembly , genome , gene , gene expression , computer science , allele , logit , machine learning
Angelica dahurica is a widely grown plant species with multiple uses, especially in the medical field. However, the frequent introduction of A . dahurica to new areas has made it difficult to distinguish between varieties. Simple sequence repeats (SSRs) detected based on transcriptome analyses are very useful for constructing genetic maps and analyzing genetic diversity. They are also relevant for the molecular marker-assisted breeding of A . dahurica . We identified 33,724 genic SSR loci based on transcriptome sequencing data. A total of 114 primer pairs were designed for the SSR loci and were tested for their specificity and diversity. Ten SSR loci in untranslated regions were ultimately selected. Subsequently, 56 A . dahurica ecotypes collected from different regions were analyzed. The SSR loci comprised 2–8 alleles, with a mean of 5.2 alleles per locus. The polymorphic information content value and Shannon’s information index were 0.6274–0.2702 (average of 0.4091) and 1.3040–0.5618 (average of 0.8475), respectively. Thus, the 10 novel SSRs identified in this study were almost in accordance with Harvey-Weinberg equilibrium and will be useful for analyzing A . dahurica genetic relationships. The results of this study confirm the potential value of transcriptome databases for the development of new SSR markers.