ArticlePhysiology and molecular biology of plants : an international journal of functional plant biology2020
Genome wide identification, characterization and validation of novel miRNA-based SSR markers in pomegranate (
Article in Physiology and molecular biology of plants : an international journal of functional plant biology, 2020. 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, 36 citations in OpenAlex.
- Development of miRNA-SSR and target-SSR markers from yield-associate genes and their applicability in the assessment of genetic diversity and association mapping in rice (Molecular breeding : new strategies in plant improvement · 2024Article
- Genome-wide characterization and development of SSR markers for genetic diversity analysis in northwestern Himalayas Walnut (3 Biotech · 2023Article
- Genome-wide survey and characterization of microsatellites in cashew and design of a web-based microsatellite database: CMDB.Frontiers in plant science · 2023Article
- Morphological, Biochemical, and Molecular Diversity of an Indian Ex Situ Collection of Pomegranate (Plants (Basel, Switzerland) · 2022Article
- Development and verification of SSR markers from drought stress-responsive miRNAs in Dongxiang wild rice (Oryza rufipogon Griff.).Functional & integrative genomics · 2022Article
- Article
- mintRULS: Prediction of miRNA-mRNA Target Site Interactions Using Regularized Least Square Method.Genes · 2022Article
- Characterization of the Spanish Pomegranate Germplasm Collection Maintained at the Agricultural Experiment Station of Elche to Identify Promising Breeding Materials.Plants (Basel, Switzerland) · 2022Article
- Chromosome-specific potential intron polymorphism markers for large-scale genotyping applications in pomegranate.Frontiers in plant science · 2022Article
- Novel miRNA-SSRs for Improving Seed Hardness Trait of Pomegranate (Frontiers in genetics · 2022Article
- Genetic Diversity ofFrontiers in plant science · 2022Article
- Targeted designing functional markers revealed the role of retrotransposon derived miRNAs as mobile epigenetic regulators in adaptation responses of pistachio.Scientific reports · 2021Article
- Article
- Comprehensive Characterization and Validation of Chromosome-Specific Highly Polymorphic SSR Markers From Pomegranate (Frontiers in plant science · 2021Article
- Development and validation of heat-responsive candidate gene and miRNA gene based SSR markers to analysis genetic diversity in wheat for heat tolerance breeding.Molecular biology reports · 2021Article
- Development of transcriptome-wide SSR markers for genetic diversity and structure analysis inPhysiology and molecular biology of plants : an international journal of functional plant biology · 2020Article
- Assessment of genetic diversity and population structure in pomegranate (Physiology and molecular biology of plants : an international journal of functional plant biology · 2020Article
Corrections and comments
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Authors and funding
8 authors at 2 institutions in 2 countries.
Funding
No grant is acknowledged in the PubMed record.
Abstract
A total of 17,439 mature miRNAs (~ 21 nt) earlier generated through RNA seq in the pomegranate were used for in silico analysis. After complexity reduction, a total of 1922 representative mature miRNAs were selected and used as query sequences against pomegranate genome to retrieve 2540 homologous contigs with flanking regions (~ 800). By using pre-miRNA prediction web server, a total of 1028 true contigs harbouring pri-miRNAs encoding 1162 pre-miRNAs were identified. Survey of these sequences for SSRs yielded a total of 1358 and 238 SSRs specific to pri-miRNA and pre-miRNAs, respectively. Of these, primer pairs were designed for 897 pri-miRNA and 168 pre-miRNA SSRs. In pri-miRNA sequences, hexa-nucleotides repeats were found to be most abundant (44.18%) followed by mono- (18.41%) and di-nucleotide (17.01%), which is also observed in pre-miRNA sequences. Further, a set of 51 randomly selected pre-miRNA-SSRs was examined for marker polymorphism. The experimental validation of these markers on eight pomegranate genotypes demonstrated 92.15% polymorphism. Utility of these functional markers was confirmed via examination of genetic diversity of 18 pomegranate genotypes using 15 miRNA-SSRs. Further, potential application of miRNA-SSRs for discovery of trait specific candidate genes was showed by validating 51 mature miRNA against publically available 2047 EST sequences of pomegranate by target and network analysis. In summary, the current study offers novel functional molecular markers for pomegranate genetic improvement.
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