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.
Highlights
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
We report the development of a high-density SNP array ‘Axiom_Arachis’ with 58 K SNPs and its utility in groundnut genetic diversity study
A high density SNP genotyping array with uniform genome coverage is must in any crop for conducting high resolution trait mapping[2,19]
Summary
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. Availability of a high-density SNP array with uniform genome coverage can advance genetic studies and breeding applications. We report the development of a high-density SNP array ‘Axiom_Arachis’ with 58 K SNPs and its utility in groundnut genetic diversity study. 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. Single nucleotide polymorphisms (SNPs) are the most abundant DNA sequence variations among various types of structural/genetic/sequence variations in the genome Until recently, it has been a tedious, labor-intensive and expensive task to develop even a limited number of SNPs. In the last decade, next-generation sequencing (NGS) technologies have evolved very rapidly and have become the cheapest and fastest method of identification of genome-wide SNPs1. Availability of draft genome sequences for both ancestral species of cultivated groundnut namely A. duranensis (A subgenome) and A. ipaensis (B subgenome) in 201617,18 is a major boost for the global groundnut research community
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