ArticleDNA research : an international journal for rapid publication of reports on genes and genomes2015
Genome-wide insertion-deletion (InDel) marker discovery and genotyping for genomics-assisted breeding applications in chickpea.
Article in DNA research : an international journal for rapid publication of reports on genes and genomes, 2015. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 31 papers, 1 of them a synthesis that pooled it.
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Who cites it
31 citing papers in PubMed, 1 synthesis or guideline pooled it, 66 citations in OpenAlex.
- Scientific evolution and translational horizons of plant core germplasm: a global bibliometric synthesis and strategic insights.Frontiers in plant science · 2026Pooled it
- Development of Genome-Derived InDel Markers and Genetic Diversity Analysis ofPlants (Basel, Switzerland) · 2026Article
- Trans-QTL Alliance of HKT1 and PHL7 Modulate Salinity Stress Tolerance and Enhance Crop Yield Endurance.Plant biotechnology journal · 2026Article
- Genomic Analysis of Indel and SV Reveals Functional and Adaptive Signatures in Hubei Indigenous Cattle Breeds.Animals : an open access journal from MDPI · 2025Article
- Genetic diversity and structure of Persicaria amphibia (Polygonaceae) in South Korea using genotyping by sequencing.Genes & genomics · 2025Article
- Identification of Insertion and Deletion (InDel) Markers for Chickpea (Plants (Basel, Switzerland) · 2024Article
- Identification of molecular markers and candidate regions associated with grain number per spike in Pubing3228 using SLAF-BSA.Frontiers in plant science · 2024Article
- Article
- Molecular Characterization and Genetic Diversity of Ginkgo (Plants (Basel, Switzerland) · 2023Article
- A superior gene allele involved in abscisic acid signaling enhances drought tolerance and yield in chickpea.Plant physiology · 2023Article
- Development of Omni InDel and supporting database for maize.Frontiers in plant science · 2023Article
- Discovery of DNA polymorphisms via genome-resequencing and development of molecular markers between two barley cultivars.Plant cell reports · 2022Article
- Development of InDel markers for Oryza sativa ssp. javanica based on whole-genome resequencing.PloS one · 2022Article
- InDel marker development and QTL analysis of agronomic traits in mung bean [Molecular breeding : new strategies in plant improvement · 2021Article
- Identification of hybridization and introgression between Cinnamomum kanehirae Hayata and C. camphora (L.) Presl using genotyping-by-sequencing.Scientific reports · 2020Article
- Genomic Analysis of Vavilov's Historic Chickpea Landraces Reveals Footprints of Environmental and Human Selection.International journal of molecular sciences · 2020Article
- A cost-effective barcode system for maize genetic discrimination based on bi-allelic InDel markers.Plant methods · 2020Article
- IDSSR: An Efficient Pipeline for Identifying Polymorphic Microsatellites from a Single Genome Sequence.International journal of molecular sciences · 2019Article
- ABC Transporter-Mediated Transport of Glutathione Conjugates Enhances Seed Yield and Quality in Chickpea.Plant physiology · 2019Article
- Article
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Authors and funding
9 authors at 2 institutions in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
We developed 21,499 genome-wide insertion-deletion (InDel) markers (2- to 54-bp in silico fragment length polymorphism) by comparing the genomic sequences of four (desi, kabuli and wild C. reticulatum) chickpea [Cicer arietinum (L.)] accessions. InDel markers showing 2- to 6-bp fragment length polymorphism among accessions were abundant (76.8%) in the chickpea genome. The physically mapped 7,643 and 13,856 markers on eight chromosomes and unanchored scaffolds, respectively, were structurally and functionally annotated. The 4,506 coding (23% large-effect frameshift mutations) and regulatory InDel markers were identified from 3,228 genes (representing 11.7% of total 27,571 desi genes), suggesting their functional relevance for trait association/genetic mapping. High amplification (97%) and intra-specific polymorphic (60-83%) potential and wider genetic diversity (15-89%) were detected by genome-wide 6,254 InDel markers among desi, kabuli and wild accessions using even a simpler cost-effective agarose gel-based assay. This signifies added advantages of this user-friendly genetic marker system for manifold large-scale genotyping applications in laboratories with limited infrastructure and resources. Utilizing 6,254 InDel markers-based high-density (inter-marker distance: 0.212 cM) inter-specific genetic linkage map (ICC 4958 × ICC 17160) of chickpea as a reference, three major genomic regions harboring six flowering and maturity time robust QTLs (16.4-27.5% phenotypic variation explained, 8.1-11.5 logarithm of odds) were identified. Integration of genetic and physical maps at these target QTL intervals mapped on three chromosomes delineated five InDel markers-containing candidate genes tightly linked to the QTLs governing flowering and maturity time in chickpea. Taken together, our study demonstrated the practical utility of developing and high-throughput genotyping of such beneficial InDel markers at a genome-wide scale to expedite genomics-assisted breeding applications in chickpea.
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Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.