ArticlePloS one2013
Global transcriptome sequencing using the Illumina platform and the development of EST-SSR markers in autotetraploid alfalfa.
Article in PloS one, 2013. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 44 papers.
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44 citing papers in PubMed, 120 citations in OpenAlex.
- Article
- Article
- Analysis on morphological characteristics and identification of candidate genes during the flowering development of alfalfa.Frontiers in plant science · 2024Article
- Potential Effect of DIMBOA (2,4-Dihydroxy-7-methoxy-1,4-benzoxazin-3-one) on Alleviating the Autotoxic Coumarin Stress in Alfalfa (Life (Basel, Switzerland) · 2022Article
- OMICS in Fodder Crops: Applications, Challenges, and Prospects.Current issues in molecular biology · 2022Review
- Transcriptome analysis and development of EST-SSR markers in Anoectochilus emeiensis (Orchidaceae).PloS one · 2022Article
- Genome-wide identification and analysis of theFrontiers in genetics · 2022Article
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- Genetic diversity and population structure analysis in a large collection of Vicia amoena in China with newly developed SSR markers.BMC plant biology · 2021Article
- Transcriptomic analysis of differentially expressed genes in leaves and roots of two alfalfa (Medicago sativa L.) cultivars with different salt tolerance.BMC plant biology · 2021Article
- Alfalfa (Medicago sativa L.) MsCML46 gene encoding calmodulin-like protein confers tolerance to abiotic stress in tobacco.Plant cell reports · 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
- A chromosome-scale genome assembly of a diploid alfalfa, the progenitor of autotetraploid alfalfa.Horticulture research · 2020Article
- Article
- Biotechnological Perspectives of Omics and Genetic Engineering Methods in Alfalfa.Frontiers in plant science · 2020Review
- De novo assembly, transcriptome characterization, and simple sequence repeat marker development in duckweedPhysiology and molecular biology of plants : an international journal of functional plant biology · 2020Article
- Transcriptome analysis of Pueraria candollei var. mirifica for gene discovery in the biosyntheses of isoflavones and miroestrol.BMC plant biology · 2019Article
- EST-SSR marker development based on RNA-sequencing of E. sibiricus and its application for phylogenetic relationships analysis of seventeen Elymus species.BMC plant biology · 2019Article
- Genetic Loci Associated with Salt Tolerance in Advanced Breeding Populations of Tetraploid Alfalfa Using Genome-Wide Association Studies.The plant genome · 2019Article
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Authors and funding
7 authors at 2 institutions in 2 countries.
Funding
No grant is acknowledged in the PubMed record.
Abstract
backgroundAlfalfa is the most widely cultivated forage legume and one of the most economically valuable crops in the world. The large size and complexity of the alfalfa genome has delayed the development of genomic resources for alfalfa research. Second-generation Illumina transcriptome sequencing is an efficient method for generating a global transcriptome sequence dataset for gene discovery and molecular marker development in alfalfa. METHODOLOGY/PRINCIPAL
findingsMore than 28 million sequencing reads (5.64 Gb of clean nucleotides) were generated by Illumina paired-end sequencing from 15 different alfalfa tissue samples. In total, 40,433 unigenes with an average length of 803 bp were obtained by de novo assembly. Based on a sequence similarity search of known proteins, a total of 36,684 (90.73%) unigenes were annotated. In addition, 1,649 potential EST-SSRs were identified as potential molecular markers from unigenes with lengths exceeding 1 kb. A total of 100 pairs of PCR primers were randomly selected to validate the assembly quality and develop EST-SSR markers from genomic DNA. Of these primer pairs, 82 were able to amplify sequences in initial screening tests, and 27 primer pairs successfully amplified DNA fragments and detected significant amounts of polymorphism among 10 alfalfa accessions. CONCLUSIONS/SIGNIFICANCE: The present study provided global sequence data for autotetraploid alfalfa and demonstrates the Illumina platform is a fast and effective approach to EST-SSR markers development in alfalfa. The use of these transcriptome datasets will serve as a valuable public information platform to accelerate studies of the alfalfa genome.
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