Peanut (Arachis hypogaea; 2n = 4x = 40) is a nutritious food and a good source of vitamins, minerals, and healthy fats. 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. For flexibility in genotyping applications, SNPs polymorphic between tetraploid and diploid species were included for use in cultivated and interspecific populations. A set of 384 accessions was used to test the array resulting in 54 564 markers that 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. Furthermore, a set of elite cultivars that make up the pedigree of US runner germplasm were genotyped and used to identify genomic regions that have undergone positive selection. These observations provide key insights on the inclusion of new genetic diversity in cultivated peanut and will inform the development of high-resolution mapping populations. Due to its efficiency, scope, and flexibility, the newly developed SNP array will be very useful for further genetic and breeding applications in Arachis.

Late leaf spot (LLS; Cercosporidium personatum) is a major fungal disease of cultivated peanut (Arachis hypogaea). A recombinant inbred line population segregating for quantitative field resistance was used to identify quantitative trait loci (QTL) using QTL-seq. High rates of false positive SNP calls using established methods in this allotetraploid crop obscured significant QTLs. To resolve this problem, robust parental SNPs were first identified using polyploid-specific SNP identification pipelines, leading to discovery of significant QTLs for LLS resistance. These QTLs were confirmed over 4 years of field data. Selection with markers linked to these QTLs resulted in a significant increase in resistance, showing that these markers can be immediately applied in breeding programs. This study demonstrates that QTL-seq can be used to rapidly identify QTLs controlling highly quantitative traits in polyploid crops with complex genomes. Markers identified can then be deployed in breeding programs, increasing the efficiency of selection using molecular tools.Key Message: Field resistance to late leaf spot is a quantitative trait controlled by many QTLs. Using polyploid-specific methods, QTL-seq is faster and more cost effective than QTL mapping.

Cultivated peanut, Arachis hypogaea L., is a tetraploid (2n = 4x = 40) species thought to be of allopolyploid origin. Its closest relatives are the diploid (2n = 2x = 20) annual and perennial species included with it in Arachis sect. Arachis. Species in section Arachis represent an important source of novel alleles for improvement of cultivated peanut. A better understanding of the level of speciation and taxonomic relationships between taxa within section Arachis is a prerequisite to the effective use of this secondary gene pool in peanut breeding programs. The AFLP technique was used to determine intra- and interspecific relationships among and within 108 accessions of 26 species of this section. A total of 1328 fragments were generated with 8 primer combinations. From those, 239 bands ranging in size from 65 to 760 bp were scored as binary data. Genetic distances among accessions ranged from 0 to 0.50. Average distances among diploid species (0.30) were much higher than that detected between tetraploid species (0.05). Cluster analysis using different methods and principal component analysis were performed. The resulting grouping of accessions and species supports previous taxonomic classifications and genome designations. Based on genetic distances and cluster analysis, A-genome accessions KG 30029 (Arachis helodes) and KSSc 36009 (Arachis simpsonii) and B-genome accession KGBSPSc 30076 (A. ipaensis) were the most closely related to both Arachis hypogaea and Arachis monticola. This finding suggests their involvement in the evolution of the tetraploid peanut species.

‘Bailey’ (Reg. No. CV‐111, PI 659502) is a large‐seeded virginia‐type peanut (Arachis hypogaea L. subsp. hypogaea var. hypogaea) with partial resistance to five diseases that occur commonly in the Virginia‐Carolina production area: early leaf spot (caused by Cercospora arachidicola Hori), late leaf spot [caused by Cercosporidium personatum (Berk. & M.A. Curtis) Deighton], Cylindrocladium black rot [caused by Cylindrocladium parasiticum Crous, M.J. Wingf. & Alfenas], Sclerotinia blight (caused by Sclerotinia minor Jagger), and tomato spotted wilt (caused by Tomato spotted wilt tospovirus). It also has partial resistance to southern stem rot (caused by Sclerotium rolfsii Sacc.). Bailey was developed as part of a program of selection for multiple‐disease resistance funded by growers, seedsmen, shellers, and processors. Bailey was tested under the experimental designation N03081T and was released by the North Carolina Agricultural Research Service (NCARS) in 2008. Bailey was tested by the NCARS, the Virginia Agricultural Experimental Station, and five other state agricultural experiment stations and the USDA‐ARS units participating in the Uniform Peanut Performance Tests. Bailey has an alternate branching pattern, an intermediate runner growth habit, medium green foliage, and high contents of fancy pods and medium virginia‐type seeds. It has approximately 34% jumbo and 46% fancy pods, seeds with tan testas and an average weight of 823 mg seed−1, and an extra large kernel content of approximately 42%. Bailey is named in honor of the late Dr. Jack E. Bailey, formerly the peanut breeding project's collaborating plant pathologist.

The genetic base of peanut (Arachis hypogaea L.) in the U