Genome Mapping By Sequencing Of The Progenitors Of The Cultivated Peanut, A. duranensis and A. ipaensis

We are generating ultra-high density genetic maps through genotyping by low coverage, shotgun sequencing of the progenitors of the cultivated peanut, A. duranensis and A. ipaensis.  These maps are being generated through sequencing the gene space of diploid and tetraploid mapping populations (~1x coverage each RIL) and of peanut diversity panels.  RIL mapping populations of the diploid wild progenitor species of both the peanut progenitor A and B genomes are being analyzed as well as a tetraploid mapping population that is derived from a cross of cultivated peanut with a synthetic amphidiploid of the two progenitor species and a cultivated peanut RIL population phenotyped for agricultural traits. In contrast to mapping-by-sequencing efforts of other species, these maps are being generated for species without an existing reference genome using a new genome mapping pipeline.  The gene space of the parental lines of each RIL population is established by sequencing of normalized genomic DNA libraries using Illumina Hiseq (60 and 20x coverage) and assembled.  Segregating SNPs are typed using survey sequencing of the mapping population.  This pipeline has been validated using the Arachis B genome and mapping the A genome is in progress.  The resultant ultra-dense maps will assist the assembly of the reference genome and provide the foundation for GWAS and QTL mapping studies.