The first high density genotyping ?Axiom_Arachis? 58K SNPs array for genetic studies and molecular breeding in groundnut uri icon

abstract

  • Genome complexity and narrow genetic base are the majorproblems that hinder achieving accelerated genetic gains ingroundnut or peanut, a major source of vegetable oil (48%)and protein (25%). High density genotyping is a must-havegenomic resource in a crop for use in several genetic andbreeding applications. Availability of genome sequence forboth the diploid genome progenitors of cultivated groundnuthas provided an opportunity for discovery of structural variationsin 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 included118,860 SNPs (58,438 SNPs for A-genome and 60,422 SNPsfor B-genome) from 30 tetraploids and 44,922 SNPs (39,937SNPs for A-genome and 4,985 SNPs for B-genome) from 11diploids. Finally, a total of 58,233 highly informative SNPs withgenome specificity were used for array development. In additionto cultivated groundnuts (Arachis hypogaea), this array hasfair representation of other diploids (A. duranensis, A. stenosperma,A. cardenasii, A. magna and A. batizocoi). Genotyping of thegroundnut ?Reference Set? containing 300 genotypes identified44,424 polymorphic SNPs and genetic diversity analysisprovided in-depth insights into the genetic architecture of thismaterial. In summary, this high-density SNP array will acceleratethe process of trait dissection and molecular breedingincluding genomic selection for achieving higher genetic gainsin groundnut

publication date

  • 2017