Genotyping tools and resources to assess peanut germplasm: smut-resistant landraces as a case study.

Alicia N Massa,Marshall C Lamb,Victor S Sobolev,Sara J Soave,Juan H Soave,Guillermo Seijo,Mario I Buteler,Renee S Arias,Claudio Oddino,Paola C Faustinelli,Marina Bressano,Valerie A Orner,Francisco J De Blas

doi:10.7717/peerj.10581

Abstract

Peanut smut caused by Thecaphora frezii is a severe fungal disease currently endemic to Argentina and Brazil. The identification of smut resistant germplasm is crucial in view of the potential risk of a global spread. In a recent study, we reported new sources of smut resistance and demonstrated its introgression into elite peanut cultivars. Here, we revisited one of these sources (line I0322) to verify its presence in the U.S. peanut germplasm collection and to identify single nucleotide polymorphisms (SNPs) potentially associated with resistance. Five accessions of Arachis hypogaea subsp. fastigiata from the U.S. peanut collection, along with the resistant source and derived inbred lines were genotyped with a 48K SNP peanut array. A recently developed SNP genotyping platform called RNase H2 enzyme-based amplification (rhAmp) was further applied to validate selected SNPs in a larger number of individuals per accession. More than 14,000 SNPs and nine rhAmp assays confirmed the presence of a germplasm in the U.S. peanut collection that is 98.6% identical (P < 0.01, bootstrap t-test) to the resistant line I0322. We report this germplasm with accompanying genetic information, genotyping data, and diagnostic SNP markers.

Highlights

Peanut smut caused by the fungus Thecaphora frezii Carranza & Lindquist is a severe soil borne disease endemic to Argentina and Brazil (Rago et al, 2017)
single nucleotide polymorphisms (SNPs) genotyping using the Axiom Arachis2 SNP array Two plants per Plant Introduction (PI) accession were grown in the greenhouse at the USDA-ARS National Peanut Research Laboratory (NPRL) in Dawson, GA, and young leaves from individual plants were used for DNA extraction
SNP genotyping with the Axiom Arachis2 SNP array Out of the 47,837 SNPs available from the 48K Axiom Arachis2 SNP array (Clevenger et al, 2018), 14,837 SNPs were successfully extracted from the PHR conversion type

Summary

Introduction

Peanut smut caused by the fungus Thecaphora frezii Carranza & Lindquist is a severe soil borne disease endemic to Argentina and Brazil (Rago et al, 2017). It was first described in a wild diploid peanut germplasm collected in Aquidauana, Mato Grosso do Sul, Brazil (Carranza & Lindquist, 1962), later identified as Arachis kuhlmannii Krapov. (Krapovickas & Gregory, 1994).

Objectives

Methods

Results

Discussion

Conclusion