Whole Genome Development of Specific Alien-Chromosome Oligo (SAO) Markers for Wild Peanut Chromosomes Based on Chorus2

The cultivated peanut (<i>Arachis hypogaea</i> L.) is a globally important oilseed and economic crop, but its narrow genetic base limits breeding progress. Wild <i>Arachis</i> species represent valuable genetic resources for enhancing the resilience of the peanut cultigen. While wild species from section <i>Arachis</i> are widely used in breeding programs, the detection of alien chromosomes in hybrids remains challenging due to limited molecular tools. In this study, a cost-effective and efficient system was established for generating species-specific molecular markers using low-coverage next-generation sequencing data, bypassing the need for whole-genome assembly. Utilizing the Chorus2 software, specific alien-chromosome oligo (SAO) markers were developed for four wild species, <i>A. duranensis</i> (accession A19), <i>A. pusilla</i> (A10), <i>A. appresipilla</i> (A33), and <i>A. glabrata</i> (G2 and G3). A total of 1166 primer pairs were designed, resulting in 220 SAO markers specific to <i>A. duranensis</i>, 77 to <i>A. pusilla</i>, 112 to <i>A. appresipilla</i>, 69 to <i>A. glabrata</i> G2, and 59 to <i>A. glabrata</i> G3, with the highest development efficiency observed in <i>A. duranensis</i> (55.0%). These markers span all chromosomes of the five wild accessions. Genome-wide, chromosome-specific SAO markers enable the efficient detection of introgressed alien chromosomes and provide insight into syntenic relationships among homoeologous chromosomes. These markers offer an effective tool for identifying favorable genes and facilitating targeted introgression for the genetic improvement of the cultivated peanut.