Novel Pipelines for Marker Discovery in Allotetraploid Arachis hypogaea Lead to Advances in Peanut Genomics

Single nucleotide polymorphism (SNP) marker discovery requires specialized strategies in polyploid genomes. Peanut, Arachis hypogaea, provides a particular challenge due to high similarity between it’s subgenomes. A pipeline, SWEEP, was developed and released that uses subgenome polymorphisms to guide detection of allelic polymorphisms between genotypes. The use of SWEEP has led to rapid advances in peanut genomics by unlocking the power of high-throughput mapping techniques such as QTL-seq and introgression mapping. Additionally, a 58K SNP array has been designed and used to obtain new insights into the diversity of US peanut elite germplasm. The array provided a large-scale SNP validation set which was mined using machine learning to provide improvements to the efficacy of SWEEP. New improvements using haplotype-based detection of polymorphisms will provide researchers of polyploid crops greater access to sequence-based genotyping methods.