ArticlePlant methods2008
Genome-wide identification of microsatellites in white clover (Trifolium repens L.) using FIASCO and phpSSRMiner.
Article in Plant methods, 2008. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 8 papers.
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Who cites it
8 citing papers in PubMed, 25 citations in OpenAlex.
- Development of Genomic Resources in MexicanGenes · 2022Article
- Genetic diversity and population structure analysis in a large collection of white clover (PeerJ · 2021Article
- Population genetic structure of Diaphorina citri Kuwayama (Hemiptera: Liviidae): host-driven genetic differentiation in China.Scientific reports · 2018Article
- Development and characterization of microsatellite markers for rice leaffolder, Cnaphalocrocis medinalis (Guenée) and cross-species amplification in other Pyralididae.Molecular biology reports · 2014Article
- An integrated genetic linkage map for white clover (Trifolium repens L.) with alignment to Medicago.BMC genomics · 2013Article
- High-resolution melting analysis for SNP genotyping and mapping in tetraploid alfalfa (Medicago sativa L.).Molecular breeding : new strategies in plant improvement · 2012Article
- QTL mapping for yield and lodging resistance in an enhanced SSR-based map for tef.TAG. Theoretical and applied genetics. Theoretische und angewandte Genetik · 2011Article
- Repertoire of SSRs in the Castor Bean Genome and Their Utilization in Genetic Diversity Analysis in Jatropha curcas.Comparative and functional genomics · 2011Article
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Authors and funding
5 authors at 1 institution in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
backgroundAllotetraploid white clover (Trifolium repens L.) is an important forage legume widely cultivated in most temperate regions. Only a small number of microsatellite markers are publicly available and can be utilized in white clover breeding programs. The objectives of this study were to develop an integrated approach for microsatellite development and to evaluate the approach for the development of new SSR markers for white clover.
resultsGenomic libraries containing simple sequence repeat (SSR) sequences were constructed using a modified Fast Isolation by AFLP of Sequences COntaining repeats (FIASCO) procedure and phpSSRMiner was used to develop the microsatellite markers. SSR motifs were isolated using two biotin-labeled probes, (CA)17 and (ATG)12. The sequences of 6,816 clones were assembled into 1,698 contigs, 32% of which represented novel sequences based on BLASTN searches. Approximately 32%, 28%, and 16% of these SSRs contained hexa-, tri-, and di-nucleotide repeats, respectively. The most frequent motifs were the CA and ATG complementary repeats and the associated compound sequences. Primer pairs were designed for 859 SSR loci based on sequences from these genomic libraries and from GenBank white clover nucleotide sequences. A total of 191 SSR primers developed from the two libraries were tested for polymorphism in individual clones from the parental genotypes GA43 ('Durana'), 'SRVR' and six F1 progeny from a mapping population. Ninety two percent produced amplicons and 66% of these were polymorphic.
conclusionThe combined approach of identifying SSR-enriched fragments by FIASCO coupled with the primer design and in silico amplification using phpSSRMiner represents an efficient and low cost pipeline for the large-scale development of microsatellite markers in plants.The approach described here could be readily adapted and utilized in other non-related species with none or limited genomic resources.
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