ArticleMolecular biology reports2012
Exploiting BAC-end sequences for the mining, characterization and utility of new short sequences repeat (SSR) markers in Citrus.
Article in Molecular biology reports, 2012. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 22 papers.
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22 citing papers in PubMed, 44 citations in OpenAlex.
- Comprehensive genome-wide identification and transferability of chromosome-specific highly variable microsatellite markers from citrus species.Scientific reports · 2023Article
- Basic Characteristics of Flower Transcriptome Data and Derived Novel EST-SSR Markers ofPlants (Basel, Switzerland) · 2022Article
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- Patterns of genetic structure and evidence of Egyptian Citrus rootstock based on informative SSR, LTR-IRAP and LTR-REMAP molecular markers.Journal, genetic engineering & biotechnology · 2021Article
- De novo transcriptomic analysis and identification of EST-SSR markers in Stephanandra incisa.Scientific reports · 2021Article
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- Transcriptome wide SSR discovery cross-taxa transferability and development of marker database for studying genetic diversity population structure of Lilium species.Scientific reports · 2020Article
- Comparative analysis of miniature inverted-repeat transposable elements (MITEs) and long terminal repeat (LTR) retrotransposons in six Citrus species.BMC plant biology · 2019Article
- Locating QTLs controlling overwintering seedling rate in perennial glutinous rice 89-1 (Oryza sativa L.).Genes & genomics · 2018Article
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- Locating QTLs controlling overwintering trait in Chinese perennial Dongxiang wild rice.Molecular genetics and genomics : MGG · 2018Article
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- Development and cross-species transferability of EST-SSR markers in Siberian wildrye (Elymus sibiricus L.) using Illumina sequencing.Scientific reports · 2016Article
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- Analysis of BAC-end sequences in common bean (Phaseolus vulgaris L.) towards the development and characterization of long motifs SSRs.Plant molecular biology · 2014Article
- Genome wide characterization of short tandem repeat markers in sweet orange (Citrus sinensis).PloS one · 2014Article
- Development of SSR markers by next-generation sequencing of Korean landraces of chamoe (Cucumis melo var. makuwa).Molecular biology reports · 2013Article
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Authors and funding
6 authors at 2 institutions in 2 countries.
Funding
No grant is acknowledged in the PubMed record.
Abstract
The aim of this study was to develop a large set of microsatellite markers based on publicly available BAC-end sequences (BESs), and to evaluate their transferability, discriminating capacity of genotypes and mapping ability in Citrus. A set of 1,281 simple sequence repeat (SSR) markers were developed from the 46,339 Citrus clementina BAC-end sequences (BES), of them 20.67% contained SSR longer than 20 bp, corresponding to roughly one perfect SSR per 2.04 kb. The most abundant motifs were di-nucleotide (16.82%) repeats. Among all repeat motifs (TA/AT)n is the most abundant (8.38%), followed by (AG/CT)n (4.51%). Most of the BES-SSR are located in the non-coding region, but 1.3% of BES-SSRs were found to be associated with transposable element (TE). A total of 400 novel SSR primer pairs were synthesized and their transferability and polymorphism tested on a set of 16 Citrus and Citrus relative's species. Among these 333 (83.25%) were successfully amplified and 260 (65.00%) showed cross-species transferability with Poncirus trifoliata and Fortunella sp. These cross-species transferable markers could be useful for cultivar identification, for genomic study of Citrus, Poncirus and Fortunella sp. Utility of the developed SSR marker was demonstrated by identifying a set of 118 markers each for construction of linkage map of Citrus reticulata and Poncirus trifoliata. Genetic diversity and phylogenetic relationship among 40 Citrus and its related species were conducted with the aid of 25 randomly selected SSR primer pairs and results revealed that citrus genomic SSRs are superior to genic SSR for genetic diversity and germplasm characterization of Citrus spp.
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