Genome-wide SNP Genotyping Resolves Signatures of Selection and Tetrasomic Recombination in Peanut

Expansion of genetic and genomic resources for genetic enhancement of cultivated peanut has gained momentum from the sequenced genomes of the diploid ancestors of cultivated peanut. To facilitate high-throughput genotyping of Arachis species, 20 genotypes were re-sequenced and genome-wide single nucleotide polymorphisms (SNPs) were selected to develop a large-scale SNP genotyping array. The array was designed to be highly flexible for Arachis, with applications for genotyping A. hypogaea populations, interspecific populations, and intraspecific diploid populations. The array included 21 547 and 22 933 markers from A. hypogaea identified relative to the A. duranensis (A) and A. ipaensis (B) genomes, respectively. The set of A. hypogaea genotypes used was selected to include important parents of research community recombinant inbred line (RIL) populations, segregating for disease resistance, biotic stress tolerance, pod characteristics, and yield, as well as globally important cultivars and parental genotypes important in India and Israel. The array also included 13 732 markers from diploid species, including 3384 polymorphic within A. duranensis species, 2389 and 2195 markers polymorphic between A genome species A. stenosperma and A. cardenasii, respectively, and 2709 and 2605 markers polymorphic between B-genome-compatible species A. batizocoi and A. magna Krapov. The utility of this array was demonstrated by assaying 384 genotypes, including elite US germplasm, the USDA mini core germplasm collection, interspecific hybrids, diploid wild species, and A. hypogaea RIL populations. By genetically following the breeding history of US runner market types, which are the most widely grown and economically important in the United States, genomic regions for which breeders have positively selected were unveiled. The results showed that the array produced high-quality polymorphic clusters between diploid species, 47 116 polymorphic markers between cultivated and interspecific hybrids, and 15 897 polymorphic markers within A. hypogaea germplasm. An additional 1193 markers were identified that illuminated genomic regions exhibiting tetrasomic recombination. The results provide key insights on the inclusion of new genetic diversity in cultivated peanut and will inform the development of high-resolution mapping populations. The newly developed SNP array will be very useful for further genetic and breeding applications in Arachis. The array's flexibility and efficiency make it an essential tool for researchers worldwide to harness genomics to improve peanut. The study utilized cultivated germplasm with importance in India, Israel, Africa, and the United States, as well as diploid wild species, to demonstrate the array's utility. The results showed that the array can be used to identify genomic regions that have undergone positive selection, which will inform the development of future populations for gene discovery. The study's findings will contribute to the improvement of peanut breeding programs and the development of new cultivars with desirable traits.