ArticleScientific reports2023
Genome-wide discovery of di-nucleotide SSR markers based on whole genome re-sequencing data of Cicer arietinum L. and Cicer reticulatum Ladiz.
Article in Scientific reports, 2023. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 7 papers.
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7 citing papers in PubMed.
- Exploring Genetic Diversity in a Temperate Bamboo: A Study Using SSR Markers.Plants (Basel, Switzerland) · 2026Article
- From gene discovery to breeding tools: functional KASP markers for flowering time selection in chickpea.BMC plant biology · 2026Article
- Identification and Development of Pathogen- and Pest-Specific Defense-Resistance-Associated SSR Marker Candidates Assisted by Machine Learning and Discovery of Putative QTL Hotspots inPlants (Basel, Switzerland) · 2026Article
- Genetic Assessment in the Andean Tropical FruitsPlants (Basel, Switzerland) · 2025Article
- Streamlining of Simple Sequence Repeat Data Mining Methodologies and Pipelines for Crop Scanning.Plants (Basel, Switzerland) · 2024Review
- Identification of Insertion and Deletion (InDel) Markers for Chickpea (Plants (Basel, Switzerland) · 2024Article
- SSR Genotyping and Marker-Trait Association with Yield Components in a Kazakh Germplasm Collection of Chickpea (Biomolecules · 2023Article
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4 authors.
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Abstract
Simple sequence repeats (SSRs) are valuable genetic markers due to their co-dominant inheritance, multi-allelic and reproducible nature. They have been largely used for exploiting genetic architecture of plant germplasms, phylogenetic analysis, and mapping studies. Among the SSRs, di-nucleotide repeats are the most frequent of the simple repeats distributed throughout the plant genomes. In present study, we aimed to discover and develop di-nucleotide SSR markers by using the whole genome re-sequencing (WGRS) data from Cicer arietinum L. and C. reticulatum Ladiz. A total of 35,329 InDels were obtained in C. arietinum, whereas 44,331 InDels in C. reticulatum. 3387 InDels with 2 bp length were detected in C. arietinum, there were 4704 in C. reticulatum. Among 8091 InDels, 58 di-nucleotide regions that were polymorphic between two species were selected and used for validation. We tested primers for evaluation of genetic diversity in 30 chickpea genotypes including C. arietinum, C. reticulatum, C. echinospermum P.H. Davis, C. anatolicum Alef., C. canariense A. Santos & G.P. Lewis, C. microphyllum Benth., C. multijugum Maesen, C. oxyodon Boiss. & Hohen. and C. songaricum Steph ex DC. A total of 244 alleles were obtained for 58 SSR markers giving an average of 2.36 alleles per locus. The observed heterozygosity was 0.08 while the expected heterozygosity was 0.345. Polymorphism information content was found to be 0.73 across all loci. Phylogenetic tree and principal coordinate analysis clearly divided the accessions into four groups. The SSR markers were also evaluated in 30 genotypes of a RIL population obtained from an interspecific cross between C. arietinum and C. reticulatum. Chi-square (χ
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