Using SNP Markers for Linkage Mapping in Diploid and Tetraploid Peanut

SNPs are attractive markers for genetic studies and marker-assisted breeding. However, scoring SNPs in polyploid plants like cultivated peanut (Arachis hypogaea L.) is problematic due to interfering signals from homeologous DNA bases. Here we used a previously constructed 1536 GoldenGate assay developed using SNPs identified between two A. duranensis accessions. In this study the performance of this assay was tested on two RIL mapping populations, one diploid (A. duranensis x A. stenosperma) and one tetraploid (A. hypogaea x synthetic tetraploid [A. ipaënsis x A. duranensis]^4x). Scoring was made using GenomeStudio 2011.1. For the diploid, default parameters gave excellent genotyping scores. In the tetraploid, as expected, most of the polymorphic markers gave signal intensity plots that were distorted compared to diploid patterns, and incorrectly scored using default parameters. However, these scorings were easily corrected in GenomeStudio software. The degree of distortion was highly variable. Of the polymorphic markers, about 10% showed no distortion at all behaving as expected for single-dose markers, another 30% showed low distortion and could be considered high quality. The genotyped markers were incorporated into diploid and tetraploid Arachis maps. In the latter case the SNP markers were located almost entirely on A genome linkage groups. This provides very graphic evidence of the highly diploid genetic behaviour of allotetraploid peanut. Selected SNPs from the assay used here can be effectively used to monitor wild introgressions into cultivated peanut on the A genome on a scale, and at a cost, that was previously impossible.