ArticleBMC plant biology2019
EST-SSR marker development based on RNA-sequencing of E. sibiricus and its application for phylogenetic relationships analysis of seventeen Elymus species.
Article in BMC plant biology, 2019. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 23 papers.
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23 citing papers in PubMed.
- Genome-Wide Development and Characterization of 169 gSSR Markers in the Invasive PlantPlants (Basel, Switzerland) · 2025Article
- Tissue-specific transcriptomic analysis reveals the molecular mechanisms responsive to cold stress in Poa crymophila, and development of EST-SSR markers linked to cold tolerance candidate genes.BMC plant biology · 2025Article
- Comparative phylogenomic study of East Asian endemic genus, Corchoropsis Siebold & Zucc. (Malvaceae s.l.), based on complete plastome sequences.BMC genomics · 2024Article
- Establishment of Novel Simple Sequence Repeat (SSR) Markers fromPlants (Basel, Switzerland) · 2024Article
- Extensive transcriptome data providing great efficacy in genetic research and adaptive gene discovery: a case study ofFrontiers in plant science · 2024Article
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- Characterization and Application of EST-SSR Markers Developed from Transcriptome Sequences inGenes · 2023Article
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- Application of MaxEnt Modeling and HRM Analysis to Support the Conservation and Domestication ofPlants (Basel, Switzerland) · 2022Article
- De novo transcriptome assembly, gene annotation, and EST-SSR marker development of an important medicinal and edible crop, Amomum tsaoko (Zingiberaceae).BMC plant biology · 2022Article
- High-Altitude Genetic Selection and Genome-Wide Association Analysis of Yield-Related Traits inFrontiers in plant science · 2022Article
- Full-length transcriptome sequencing analysis and characterization, development and validation of microsatellite markers inFrontiers in plant science · 2022Article
- De novo transcriptome assembly and EST-SSR markers development for Zelkova schneideriana Hand.-Mazz. (Ulmaceae).3 Biotech · 2021Article
- Protocol development for somatic embryogenesis, SSR markers and genetic modification of Stipagrostis pennata (Trin.) De Winter.Plant methods · 2021Article
- Transcriptomic resources for prairie grass (Bromus catharticus): expressed transcripts, tissue-specific genes, and identification and validation of EST-SSR markers.BMC plant biology · 2021Article
- The development of SSR markers based on RNA-sequencing and its validation between and within Carex L. species.BMC plant biology · 2021Article
- Development of EST-SSR Markers Linked to Flowering Candidate Genes inPlants (Basel, Switzerland) · 2020Article
- Development of EST-SSR markers and association mapping with floral traits in Syringa oblata.BMC plant biology · 2020Article
- Estimation of genetic diversity and population structure in3 Biotech · 2020Article
- Article
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8 authors.
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No grant is acknowledged in the PubMed record.
Abstract
backgroundElymus L. is the largest genus in the tribe Triticeae Dumort., encompassing approximately 150 polyploid perennial species widely distributed in the temperate regions of the world. It is considered to be an important gene pool for improving cereal crops. However, a shortage of molecular marker limits the efficiency and accuracy of genetic breeding for Elymus species. High-throughput transcriptome sequencing data is essential for gene discovery and molecular marker development.
resultsWe obtained the transcriptome dataset of E. sibiricus, the type species of the genus Elymus, and identified a total of 8871 putative EST-SSRs from 6685 unigenes. Trinucleotides were the dominant repeat motif (4760, 53.66%), followed by dinucleotides (1993, 22.47%) and mononucleotides (1876, 21.15%). The most dominant trinucleotide repeat motif was CCG/CGG (1119, 23.5%). Sequencing of PCR products showed that the sequenced alleles from different Elymus species were homologous to the original SSR locus from which the primer was designed. Different types of tri-repeats as abundant SSR motifs were observed in repeat regions. Two hundred EST-SSR primer pairs were designed and selected to amplify ten DNA samples of Elymus species. Eighty-seven pairs of primer (43.5%) generated clear and reproducible bands with expected size, and showed good transferability across different Elymus species. Finally, thirty primer pairs successfully amplified ninety-five accessions of seventeen Elymus species, and detected significant amounts of polymorphism. In general, hexaploid Elymus species with genomes StStHHYY had a relatively higher level of genetic diversity (H = 0.219, I = 0.330, %P = 63.7), while tetraploid Elymus species with genomes StStYY had low level of genetic diversity (H = 0.182, I = 0.272, %P = 50.4) in the study. The cluster analysis showed that all ninety-five accessions were clustered into three major clusters. The accessions were grouped mainly according to their genomic components and origins.
conclusionsThis study demonstrated that transcriptome sequencing is a fast and cost-effective approach to molecular marker development. These EST-SSR markers developed in this study are valuable tools for genetic diversity, evolutionary, and molecular breeding in E. sibiricus, and other Elymus species.
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