Molecular marker development from transcript sequences and germplasm evaluation for cultivated peanut (Arachis hypogaea L.)

Mol Genet Genomics. 2016 Feb;291(1):363-81. doi: 10.1007/s00438-015-1115-6. Epub 2015 Sep 11.


Molecular markers are important tools for genotyping in genetic studies and molecular breeding. The SSR and SNP are two commonly used marker systems developed from genomic or transcript sequences. The objectives of this study were to: (1) assemble and annotate the publicly available ESTs in Arachis and the in-house short reads, (2) develop and validate SSR and SNP markers, and (3) investigate the genetic diversity and population structure of the peanut breeding lines and the U.S. peanut mini core collection using developed SSR markers. An NCBI EST dataset with 252,951 sequences and an in-house 454 RNAseq dataset with 288,701 sequences were assembled separately after trimming. Transcript sequence comparison and phylogenetic analysis suggested that peanut is closer to cowpea and scarlet bean than to soybean, common bean and Medicago. From these two datasets, 6455 novel SSRs and 11,902 SNPs were identified. Of the discovered SSRs, 380 representing various SSR types were selected for PCR validation. The amplification rate was 89.2 %. Twenty-two (6.5 %) SSRs were polymorphic between at least one pair of four genotypes. Sanger sequencing of PCR products targeting 110 SNPs revealed 13 true SNPs between tetraploid genotypes and 193 homoeologous SNPs within genotypes. Eight out of the 22 polymorphic SSR markers were selected to evaluate the genetic diversity of Florida peanut breeding lines and the U.S. peanut mini core collection. This marker set demonstrated high discrimination power by displaying an average polymorphism information content value of 0.783, a combined probability of identity of 10(-11), and a combined power of exclusion of 0.99991. The structure analysis revealed four sub-populations among the peanut accessions and lines evaluated. The results of this study enriched the peanut genomic resources, provided over 6000 novel SSR markers and the credentials for true peanut SNP marker development, and demonstrated the power of newly developed SSR markers in genotyping peanut germplasm and breeding materials.

Keywords: Diversity; Marker; Peanut; Polymorphism; SNP; SSR; Transcript.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Arachis / genetics*
  • Chromosome Mapping / methods
  • DNA, Plant / genetics
  • Expressed Sequence Tags / metabolism
  • Genetic Markers / genetics*
  • Genetic Variation / genetics
  • Genome, Plant / genetics
  • Genotype
  • Microsatellite Repeats / genetics
  • Phylogeny
  • Polymorphism, Single Nucleotide / genetics
  • Sequence Analysis, DNA / methods
  • Tetraploidy


  • DNA, Plant
  • Genetic Markers