Genome-wide insertion–deletion (InDel) marker discovery and genotyping for genomics-assisted breeding applications in chickpea
| Autor: | Shouvik Das, Shivali Sharma, Deepak Bajaj, Rishi Srivastava, Sube Singh, Akhilesh K. Tyagi, Hari D. Upadhyaya, C. L. L. Gowda, Swarup K. Parida |
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| Rok vydání: | 2015 |
| Předmět: |
Genetic Markers
Genotyping Techniques Genetic Linkage QTL Molecular Sequence Data Quantitative Trait Loci Quantitative trait locus Biology Polymorphism Single Nucleotide INDEL Mutation Gene mapping chickpea Genetics Indel Molecular Biology Genotyping Genetic diversity Base Sequence Chromosome Mapping food and beverages Genomics Sequence Analysis DNA flowering time General Medicine Full Papers Cicer Plant Breeding Genetic marker maturity time InDel Genome Plant |
| Zdroj: | DNA Research: An International Journal for Rapid Publication of Reports on Genes and Genomes |
| ISSN: | 1756-1663 1340-2838 |
| DOI: | 10.1093/dnares/dsv020 |
| Popis: | 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. |
| Databáze: | OpenAIRE |
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