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The first high density genotyping ‘Axiom_Arachis’ 58K SNPs array for genetic studies and molecular breeding in groundnut

Pandey, M.K., Agarwal, G., Kale, S.M., Clevenger, J., Nayak, S.N., Sriswathi, M., Chitikineni, A., Chavarro, C., Chen, X., Upadhyaya, H.D., Vishwakarma, M.K., Leal-Bertioli, S., Liang, X., Bertioli, D.J., Guo, B., Jackson, S.A., Ozias-Akins, P. and Varshney, R.K.ORCID: 0000-0002-4562-9131 (2017) The first high density genotyping ‘Axiom_Arachis’ 58K SNPs array for genetic studies and molecular breeding in groundnut. In: InterDrought-V, 21 - 25 February 2017, Hyderabad, India.


Genome complexity and narrow genetic base are the major problems that hinder achieving accelerated genetic gains in groundnut or peanut, a major source of vegetable oil (48%) and protein (25%). High density genotyping is a must-have genomic resource in a crop for use in several genetic and breeding applications. Availability of genome sequence for both the diploid genome progenitors of cultivated groundnut has provided an opportunity for discovery of structural variations in large-scale including single nucleotide polymorphisms (SNPs), the most abundant DNA sequence variation in the genomes. In this context, we developed a high-density SNP array ‘Axiom_Arachis’ with 58K SNPs with uniform genome coverage. We identified initially a total of 163,782 SNPs that included 118,860 SNPs (58,438 SNPs for A-genome and 60,422 SNPs for B-genome) from 30 tetraploids and 44,922 SNPs (39,937 SNPs for A-genome and 4,985 SNPs for B-genome) from 11 diploids. Finally, a total of 58,233 highly informative SNPs with genome specificity were used for array development. In addition to cultivated groundnuts (Arachis hypogaea), this array has fair representation of 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. In summary, this high-density SNP array will accelerate the process of trait dissection and molecular breeding including genomic selection for achieving higher genetic gains in groundnut.

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