Late leaf spot (LLS) is a major foliar disease that significantly reduces yield and compromises the quality of peanut (Arachis hypogaea L.). To identify genes conferring LLS resistance, a recombinant inbred line (RIL) population of 257 lines from a cross between the susceptible cultivar Baisha 1016 and the resistant germplasm ICGV 86699 was analyzed using whole-genome resequencing. A high-density genetic map was constructed with 4908 bin markers, leading to the identification of 19 quantitative trait loci (QTL) for LLS resistance. A major QTL, qLLS.A02.1, was consistently detected on chromosome A02 across six environments, explaining up to 37.49% of the phenotypic variance. Fine mapping delimited the qLLS.A02.1 locus to a 319 kb region flanked by KASP markers S4 and S5, which contained a cluster of ten NBS-LRR genes. Validation in 266 accessions confirmed a significant association of these flanking markers with LLS resistance. Transcriptome analysis revealed that four NBS-LRR genes within the cluster were specifically upregulated in the resistant parent. This study provides valuable genetic resources and molecular markers for breeding LLS-resistant peanut varieties.

Superoxide dismutase (SOD, EC 1.15.1.1) plays a key role in response to drought stress, and differences in SOD activity changes among cultivars are important under drought conditions. We obtained the full-length DNA of the chloroplast Cu/Zn-SOD gene (AhCSD2) from 11 allotetraploid cultivars and 5 diploid wild species in peanut. BLAST search against the peanut genome showed that the AhCSD2 genes gCSD2-1 and gCSD2-2 are located at the tops of chromosome A03 (A genome) and B03 (B genome), respectively, and both contain 8 exons and 7 introns. Nucleotide sequence analyses indicated that gCSD2-2 sequences were identical among all the tested cultivars, while gCSD2-1 sequences showed allelic variations. The amino acid sequences deduced from gCSD2-1 and gCSD2-2 both contain a chloroplast transit peptide and are distinguished by 6 amino acid (aa) residue differences. The other 2 aa residue variations in the mature peptide regions give rise to three-dimensional structure changes of the protein deduced from the genes gCSD2-1 and gCSD2-2. Sequences analyses of cultivars and wild species showed that gCSD2-2 of Arachis hypogaea and gAipCSD2 (Arachis ipaensis) are identical, and despite the abundant polymorphic loci between gCSD2-1 of A. hypogaea and sequences from A genome wild species, the deduced amino acid sequence of AhCSD2-1 (A. hypogaea) is identical to that of AduCSD2 (Arachis duranensis), whereas AcoCSD2 (Arachis correntina) and AcaCSD2 (Arachis cardenasii) both have 2 aa differences in the transit peptide region compared with AhCSD2-1 (A. hypogaea). Based on the Peanut Genome Project, promoter prediction revealed many stress-related cis-acting elements within the potential promoter regions (pp-A and pp-B). pp-A contains more binding sites for drought-associated transcriptional factors than pp-B. We hypothesize that the marked changes in SOD activity in different cultivars under drought stress are tightly regulated by transcription factors through transcription and expression of AhCSD2 genes.