Abstract
Groundnut, an allotetraploid legume crop, serves as an important source of food, feed, and confectioneries worldwide. Translational genomics research has accelerated precision breeding efforts in groundnut using marker-assisted and genomic selection approaches. To support these efforts, three cost-effective and high-throughput genotyping panels have been developed to facilitate genetic studies and breeding applications. We developed high density genotyping array with 58K SNP markers which has been extensively used by global peanut research community. The first mid-density genotyping assay, comprises 5081 SNP markers, including 5000 highly informative SNPs with high polymorphism information content (PIC) derived from previously developed high-density ‘Axiom_Arachis’ array of 58,233 SNPs. An additional 81 SNPs associated with resilience and quality traits were incorporated for marker-assisted selection. This panel demonstrated robust performance, with PIC values ranging from 0.34 to 0.37 and explained 82.08% of genetic variance across 2573 genotypes from diverse sets of breeding populations. This panel holds promise for possible deployment in the identification of varietal seed mixture, genetic purity within gene bank germplasms and seed systems, foreground and background selection in backcross breeding programs, genomic selection, and sparse trait mapping studies in groundnut. The second panel, a mid-density array of 2500 SNP markers with an average density of 1 SNP per Mbp, is powerful tool for global groundnut breeding programmes. These SNPs were identified through whole-genome resequencing of 263 cultivated groundnut accessions representing diverse agronomic types and geographical regions. The panel includes 20-quality control (QC) and 72 associated markers for 8 key traits, namely leaf rust resistance, late leaf spot resistance, net blotch resistance, high oleic acid, seed weight, shelling percentage, fresh seed dormancy and blanchability. Designed through rigorous filtering processes, this panel is particularly suited for marker-assisted backcrossing, diversity analyses, and to study genetic purity for efficient germplasm management. Together, these genotyping panels provide versatile tools for advancing groundnut breeding programs, enabling precise and efficient genetic interventions for sustainable crop improvement.