Pandey, M K and Agarwal, G and Kale, S M and Clevenger, J and Nayak, S N and Sriswathi, M and Chitikineni, A and Chavarro, C and Chen, X and Upadhyaya, H D and Vishwakarma, M K and Leal-Bertioli, S and Liang, X and Bertioli, D J and Guo, B and Jackson, S A and Ozias-Akins, P and Varshney, R K (2017) Development and Evaluation of a High Density Genotyping ‘Axiom_Arachis’ Array with 58 K SNPs for Accelerating Genetics and Breeding in Groundnut. Scientific Reports, 7. pp. 1-10. ISSN 2045-2322
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Abstract
Single nucleotide polymorphisms (SNPs) are the most abundant DNA sequence variation in the genomes which can be used to associate genotypic variation to the phenotype. Therefore, availability of a high-density SNP array with uniform genome coverage can advance genetic studies and breeding applications. Here we report the development of a high-density SNP array ‘Axiom_Arachis’ with 58 K SNPs and its utility in groundnut genetic diversity study. In this context, from a total of 163,782 SNPs derived from DNA resequencing and RNA-sequencing of 41 groundnut accessions and wild diploid ancestors, a total of 58,233 unique and informative SNPs were selected for developing the array. In addition to cultivated groundnuts (Arachis hypogaea), fair representation was kept for other diploids (A. duranensis, A. stenosperma, A. cardenasii, A. magna and A. batizocoi). Genotyping of the groundnut ‘Reference Set’ containing 300 genotypes identified 44,424 polymorphic SNPs and genetic diversity analysis provided in-depth insights into the genetic architecture of this material. The availability of the high-density SNP array ‘Axiom_Arachis’ with 58 K SNPs will accelerate the process of high resolution trait genetics and molecular breeding in cultivated groundnut.
| Item Type: | Article |
|---|---|
| Divisions: | Research Program : Genetic Gains |
| CRP: | CGIAR Research Program on Grain Legumes |
| Uncontrolled Keywords: | Single nucleotide polymorphisms, SNPs, DNA sequence variation, Breeding, Groundnut, Peanut, Genetic analysis |
| Subjects: | Others > Plant Breeding Mandate crops > Groundnut Others > Genetics and Genomics |
| Depositing User: | Mr Ramesh K |
| Date Deposited: | 14 Apr 2017 04:39 |
| Last Modified: | 17 May 2017 10:15 |
| URI: | http://oar.icrisat.org/id/eprint/9960 |
| Official URL: | http://dx.doi.org/10.1038/srep40577 |
| Projects: | UNSPECIFIED |
| Funders: | Bill & Melinda Gates Foundation (Tropical Legumes III), MARS Chocolate Inc., & The Peanut Foundation |
| Acknowledgement: | The authors are thankful to Bill & Melinda Gates Foundation (Tropical Legumes III), MARS Chocolate Inc., and The Peanut Foundation for financial assistance. 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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