Abundant microsatellite diversity and oil content in wild Arachis species

PLoS One. 2012;7(11):e50002. doi: 10.1371/journal.pone.0050002. Epub 2012 Nov 20.


The peanut (Arachis hypogaea) is an important oil crop. Breeding for high oil content is becoming increasingly important. Wild Arachis species have been reported to harbor genes for many valuable traits that may enable the improvement of cultivated Arachis hypogaea, such as resistance to pests and disease. However, only limited information is available on variation in oil content. In the present study, a collection of 72 wild Arachis accessions representing 19 species and 3 cultivated peanut accessions were genotyped using 136 genome-wide SSR markers and phenotyped for oil content over three growing seasons. The wild Arachis accessions showed abundant diversity across the 19 species. A. duranensis exhibited the highest diversity, with a Shannon-Weaver diversity index of 0.35. A total of 129 unique alleles were detected in the species studied. A. rigonii exhibited the largest number of unique alleles (75), indicating that this species is highly differentiated. AMOVA and genetic distance analyses confirmed the genetic differentiation between the wild Arachis species. The majority of SSR alleles were detected exclusively in the wild species and not in A. hypogaea, indicating that directional selection or the hitchhiking effect has played an important role in the domestication of the cultivated peanut. The 75 accessions were grouped into three clusters based on population structure and phylogenic analysis, consistent with their taxonomic sections, species and genome types. A. villosa and A. batizocoi were grouped with A. hypogaea, suggesting the close relationship between these two diploid wild species and the cultivated peanut. Considerable phenotypic variation in oil content was observed among different sections and species. Nine alleles were identified as associated with oil content based on association analysis, of these, three alleles were associated with higher oil content but were absent in the cultivated peanut. The results demonstrated that there is great potential to increase the oil content in A. hypogaea by using the wild Arachis germplasm.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Alleles
  • Arachis* / chemistry
  • Arachis* / genetics
  • DNA, Plant
  • Genome, Plant
  • Genotype
  • Microsatellite Repeats / genetics*
  • Phylogeny
  • Plant Oils / chemistry*
  • Polymorphism, Genetic
  • Sequence Analysis, DNA
  • Species Specificity


  • DNA, Plant
  • Plant Oils

Grant support

The authors are grateful to the research grants from the National Basic Research Program of China (2011CB109300) and Crop Germplasm Program (NB09-2130135-4) and the National Science Fund of China (No. 31271764). The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.