ArticleDNA research : an international journal for rapid publication of reports on genes and genomes2013
Development and application of microsatellites in candidate genes related to wood properties in the Chinese white poplar (Populus tomentosa Carr.).
Article in DNA research : an international journal for rapid publication of reports on genes and genomes, 2013. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 17 papers.
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17 citing papers in PubMed, 39 citations in OpenAlex.
- Article
- PtoNF-YC9-SRMT-PtoRD26 module regulates the high saline tolerance of a triploid poplar.Genome biology · 2022Article
- Cloning and characterization of KoOsmotin from mangrove plant Kandelia obovata under cold stress.BMC plant biology · 2021Article
- Characteristics of Microsatellites Mined from Transcriptome Data and the Development of Novel Markers inGenes · 2020Article
- Article
- Transcriptome-wide identification of miRNA targets and a TAS3-homologous gene in Populus by degradome sequencing.Genes & genomics · 2019Article
- The first identification of genomic loci in plants associated with resistance to galling insects: a case study in Eucalyptus L'Hér. (Myrtaceae).Scientific reports · 2018Article
- Genome-wide identification and characterization of novel lncRNAs in Populus under nitrogen deficiency.Molecular genetics and genomics : MGG · 2016Article
- Molecular Cloning and Characterization of O-Methyltransferase from Mango Fruit (Mangifera indica cv. Alphonso).Molecular biotechnology · 2016Article
- De novo assembly and characterization of the leaf, bud, and fruit transcriptome from the vulnerable tree Juglans mandshurica for the development of 20 new microsatellite markers using Illumina sequencing.Molecular genetics and genomics : MGG · 2016Article
- Transcriptome Sequencing and Development of Genic SSR Markers of an Endangered Chinese Endemic Genus Dipteronia Oliver (Aceraceae).Molecules (Basel, Switzerland) · 2016Article
- The genetic regulatory network centered on Pto-Wuschela and its targets involved in wood formation revealed by association studies.Scientific reports · 2015Article
- Transcriptome-Wide Identification of miRNA Targets under Nitrogen Deficiency in Populus tomentosa Using Degradome Sequencing.International journal of molecular sciences · 2015Article
- Application of Microsatellite Loci for Molecular Identification of Elite Genotypes, Analysis of Clonality, and Genetic Diversity in Aspen Populus tremula L. (Salicaceae).International journal of plant genomics · 2015Article
- Exploiting transcriptome data for the development and characterization of gene-based SSR markers related to cold tolerance in oil palm (Elaeis guineensis).BMC plant biology · 2014Article
- Genome-wide microsatellite characterization and marker development in the sequenced Brassica crop species.DNA research : an international journal for rapid publication of reports on genes and genomes · 2014Article
- Article
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4 authors at 2 institutions in 2 countries.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Gene-derived simple sequence repeats (genic SSRs), also known as functional markers, are often preferred over random genomic markers because they represent variation in gene coding and/or regulatory regions. We characterized 544 genic SSR loci derived from 138 candidate genes involved in wood formation, distributed throughout the genome of Populus tomentosa, a key ecological and cultivated wood production species. Of these SSRs, three-quarters were located in the promoter or intron regions, and dinucleotide (59.7%) and trinucleotide repeat motifs (26.5%) predominated. By screening 15 wild P. tomentosa ecotypes, we identified 188 polymorphic genic SSRs with 861 alleles, 2-7 alleles for each marker. Transferability analysis of 30 random genic SSRs, testing whether these SSRs work in 26 genotypes of five genus Populus sections (outgroup, Salix matsudana), showed that 72% of the SSRs could be amplified in Turanga and 100% could be amplified in Leuce. Based on genotyping of these 26 genotypes, a neighbour-joining analysis showed the expected six phylogenetic groupings. In silico analysis of SSR variation in 220 sequences that are homologous between P. tomentosa and Populus trichocarpa suggested that genic SSR variations between relatives were predominantly affected by repeat motif variations or flanking sequence mutations. Inheritance tests and single-marker associations demonstrated the power of genic SSRs in family-based linkage mapping and candidate gene-based association studies, as well as marker-assisted selection and comparative genomic studies of P. tomentosa and related species.
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