Vishwakarma, M K and Kale, S M and Sriswathi, M and Naresh, T and Shasidhar, Y and Garg, V and Pandey, M K and Varshney, R K (2017) Genome-Wide Discovery and Deployment of Insertions and Deletions Markers Provided Greater Insights on Species, Genomes, and Sections Relationships in the Genus Arachis. Frontiers in Plant Science, 8 (2064). pp. 1-13. ISSN 1664-462X
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Abstract
Small insertions and deletions (InDels) are the second most prevalent and the most abundant structural variations in plant genomes. In order to deploy these genetic variations for genetic analysis in genus Arachis, we conducted comparative analysis of the draft genome assemblies of both the diploid progenitor species of cultivated tetraploid groundnut (Arachis hypogaea L.) i.e., Arachis duranensis (A subgenome) and Arachis ipaënsis (B subgenome) and identified 515,223 InDels. These InDels include 269,973 insertions identified in A. ipaënsis against A. duranensis while 245,250 deletions in A. duranensis against A. ipaënsis. The majority of the InDels were of single bp (43.7%) and 2–10 bp (39.9%) while the remaining were >10 bp (16.4%). Phylogenetic analysis using genotyping data for 86 (40.19%) polymorphic markers grouped 96 diverse Arachis accessions into eight clusters mostly by the affinity of their genome. This study also provided evidence for the existence of “K” genome, although distinct from both the “A” and “B” genomes, but more similar to “B” genome. The complete homology between A. monticola and A. hypogaea tetraploid taxa showed a very similar genome composition. The above analysis has provided greater insights into the phylogenetic relationship among accessions, genomes, sub species and sections. These InDel markers are very useful resource for groundnut research community for genetic analysis and breeding applications.
| Item Type: | Article |
|---|---|
| Divisions: | Research Program : Genetic Gains |
| CRP: | CGIAR Research Program on Grain Legumes |
| Uncontrolled Keywords: | Arachis, InDel, genomes, phylogeny, sections, Genome Sequences, Genome-Wide Indels Discovery, Genetic Diversity |
| Subjects: | Others > Genetics and Genomics |
| Depositing User: | Mr Ramesh K |
| Date Deposited: | 21 Dec 2017 09:10 |
| Last Modified: | 21 Dec 2017 09:10 |
| URI: | http://oar.icrisat.org/id/eprint/10370 |
| Official URL: | http://dx.doi.org/10.3389/fpls.2017.02064 |
| Projects: | UNSPECIFIED |
| Funders: | UNSPECIFIED |
| Acknowledgement: | The authors are thankful to The Peanut Foundation, Bill, and Melinda Gates Foundation (Tropical Legumes III) and MARS Chocolate Inc., USA, and World Bank-assisted Karnataka Watershed Development Project-II (KWDP-II) funded by Government of Karnataka (GoK), India for financial assistance. Authors are thankful to Dr. Hari D. Upadhyaya for providing seeds of genotypes included in the study. The work reported in this article was undertaken as a part of the CGIAR Research Program on Grain Legumes. ICRISAT is a member of the CGIAR. |
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