Journal article
Development and evaluation of a high density genotyping ‘Axiom_Arachis’ array with 58 K SNPs for accelerating genetics and breeding in groundnut
Scientific Report, Vol.7(1), Art. 40577
2017
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.
Details
- Title
- Development and evaluation of a high density genotyping ‘Axiom_Arachis’ array with 58 K SNPs for accelerating genetics and breeding in groundnut
- Authors/Creators
- M.K. Pandey (Author/Creator) - International Crops Research Institute for the Semi-Arid TropicsG. Agarwal (Author/Creator) - International Crops Research Institute for the Semi-Arid TropicsS.M. Kale (Author/Creator) - International Crops Research Institute for the Semi-Arid TropicsJ. Clevenger (Author/Creator) - University of GeorgiaS.N. Nayak (Author/Creator) - International Crops Research Institute for the Semi-Arid TropicsM. Sriswathi (Author/Creator) - International Crops Research Institute for the Semi-Arid TropicsA. Chitikineni (Author/Creator) - International Crops Research Institute for the Semi-Arid TropicsC. Chavarro (Author/Creator) - Applied Genetic Technologies (United States)X. Chen (Author/Creator) - Guangdong Academy of Agricultural SciencesH.D. Upadhyaya (Author/Creator) - International Crops Research Institute for the Semi-Arid TropicsM.K. Vishwakarma (Author/Creator) - International Crops Research Institute for the Semi-Arid TropicsS. Leal-Bertioli (Author/Creator)X. Liang (Author/Creator) - Guangdong Academy of Agricultural SciencesD.J. Bertioli (Author/Creator) - Applied Genetic Technologies (United States)B. Guo (Author/Creator) - Agricultural Research ServiceS.A. Jackson (Author/Creator) - Applied Genetic Technologies (United States)P. Ozias-Akins (Author/Creator) - University of GeorgiaR.K. Varshney (Author/Creator) - International Crops Research Institute for the Semi-Arid Tropics
- Publication Details
- Scientific Report, Vol.7(1), Art. 40577
- Publisher
- Springer Nature
- Identifiers
- 991005542253107891
- Copyright
- © 2017 The Authors.
- Murdoch Affiliation
- Murdoch University
- Language
- English
- Resource Type
- Journal article
UN Sustainable Development Goals (SDGs)
This output has contributed to the advancement of the following goals:
Source: InCites
Metrics
32 File views/ downloads
43 Record Views
InCites Highlights
These are selected metrics from InCites Benchmarking & Analytics tool, related to this output
- Collaboration types
- Domestic collaboration
- International collaboration
- Citation topics
- 3 Agriculture, Environment & Ecology
- 3.4 Crop Science
- 3.4.96 QTL
- Web Of Science research areas
- Genetics & Heredity
- ESI research areas
- Molecular Biology & Genetics