ArticlePloS one2014
Development and characterization of simple sequence repeat (SSR) markers based on RNA-sequencing of Medicago sativa and in silico mapping onto the M. truncatula genome.
Article in PloS one, 2014. The graph could read no effect estimate from its abstract, so it casts no vote on the map. An erratum has been issued. Cited by 22 papers.
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Who cites it
22 citing papers in PubMed, 62 citations in OpenAlex.
- RNA-Seq-based transcriptomics reveals differential gene expression between two Pisum sativum subspecies and uncovers their molecular marker profiles.BMC genomics · 2025Article
- Morphological diversity variation of seed traits among 587 germplasm resources of Medicago Genus and 32 germplasm resources of Trigonella Genus.Scientific reports · 2025Article
- Population genetic variation and geographic distribution of suitable areas ofFrontiers in plant science · 2024Article
- Development of EST-SSR markers based on transcriptome sequencing for germplasm evaluation of 65 lilies (Lilium).Molecular biology reports · 2023Article
- Article
- Eco-Geographical, Morphological and Molecular Characterization of a Collection of the Perennial Endemic SpeciesPlants (Basel, Switzerland) · 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 for genetic diversity analysis in coconut (Cocos nucifera L.).Molecular biology reports · 2020Article
- Cross-genera amplification ofPhysiology and molecular biology of plants : an international journal of functional plant biology · 2020Article
- Development of EST-SSR markers forPhysiology and molecular biology of plants : an international journal of functional plant biology · 2020Article
- Development of EST-SSR Markers Linked to Flowering Candidate Genes inPlants (Basel, Switzerland) · 2020Article
- Article
- Identification and characterization of SSR, SNP and InDel molecular markers from RNA-Seq data of guar (Cyamopsis tetragonoloba, L. Taub.) roots.BMC genomics · 2018Article
- Mining and Development of Novel SSR Markers Using Next Generation Sequencing (NGS) Data in Plants.Molecules (Basel, Switzerland) · 2018Review
- In Silico development of new SSRs primer for aquaporin linked to drought tolerance in plants.Plant signaling & behavior · 2018Article
- Transcriptome analysis of the Chinese giant salamander (Genomics data · 2017Article
- RNA-Sequencing Reveals Biological Networks during Table Grapevine ('Fujiminori') Fruit Development.PloS one · 2017Article
- RNA-Seq of Guar (Frontiers in plant science · 2017Article
- Transcriptome Sequencing and Development of Genic SSR Markers of an Endangered Chinese Endemic Genus Dipteronia Oliver (Aceraceae).Molecules (Basel, Switzerland) · 2016Article
- Article
Corrections and comments
- Erratum issued
Authors and funding
6 authors at 1 institution in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Sufficient codominant genetic markers are needed for various genetic investigations in alfalfa since the species is an outcrossing autotetraploid. With the newly developed next generation sequencing technology, a large amount of transcribed sequences of alfalfa have been generated and are available for identifying SSR markers by data mining. A total of 54,278 alfalfa non-redundant unigenes were assembled through the Illumina HiSeqTM 2000 sequencing technology. Based on 3,903 unigene sequences, 4,493 SSRs were identified. Tri-nucleotide repeats (56.71%) were the most abundant motif class while AG/CT (21.7%), AGG/CCT (19.8%), AAC/GTT (10.3%), ATC/ATG (8.8%), and ACC/GGT (6.3%) were the subsequent top five nucleotide repeat motifs. Eight hundred and thirty- seven EST-SSR primer pairs were successfully designed. Of these, 527 (63%) primer pairs yielded clear and scored PCR products and 372 (70.6%) exhibited polymorphisms. High transferability was observed for ssp falcata at 99.2% (523) and 71.7% (378) in M. truncatula. In addition, 313 of 527 SSR marker sequences were in silico mapped onto the eight M. truncatula chromosomes. Thirty-six polymorphic SSR primer pairs were used in the genetic relatedness analysis of 30 Chinese alfalfa cultivated accessions generating a total of 199 scored alleles. The mean observed heterozygosity and polymorphic information content were 0.767 and 0.635, respectively. The codominant markers not only enriched the current resources of molecular markers in alfalfa, but also would facilitate targeted investigations in marker-trait association, QTL mapping, and genetic diversity analysis in alfalfa.
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