Development and evaluation of a high density genotyping ‘Axiom_Arachis’ array with 58K SNPs for accelerating genetics and breeding in groundnut

Summary

Single nucleotide polymorphisms (SNPs) are the most abundant DNA sequence variation in  genomes, and can be used to associate genotypic variation in phenotypes. Therefore, the availability of a high-density SNP array with uniform genome coverage can advance genetic studies and breeding applications. The article discusses the development of a high-density SNP array ‘Axiom_Arachis’ with 58 K SNPs and its utility in a 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 58K SNPs will accelerate the process of high resolution trait genetics and molecular breeding in cultivated groundnut.

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