Late leaf spot (LLS) disease caused by Nothopassalora personata (Berk. & M.A. Curtis) U. Braun, C. Nakash, Videira & Crous is prevalent among pathogens encountered in peanut (Arachis hypogaea L.) growing regions. Chemical control is expensive, sometimes inaccessible, and can be difficult to apply. One effective solution to control this disease is the deployment of resistant cultivars. IAC 322 is a breeding line resistant to foliar fungal disease and harbors alien introgressions from A. cardenasii Krapov. & W.C. Gregory, a wild diploid relative of peanut. The objective of this study was to determine the level of LLS resistance conferred by introgressed segments in families derived from TifNV‐High O/L × IAC 322. Phenotyping for LLS resistance was performed under both in vitro and field conditions, which provided sufficient disease pressure to separate the means of susceptible and resistant checks, although there was no statistically significant separation of LLS resistance among the families with introgressions. However, consistent levels of LLS resistance observed in the family with A02‐top/A03‐bottom segments makes it a valuable resource for peanut breeding. In addition, late‐season field disease ratings were found to correlate with the entire LLS infection progression under both field and in vitro conditions. Among the parameters collected for in vitro experiments, numbers of LLS lesions and sporulating LLS lesions at late stages of LLS infection and incubation period can be used to predict LLS resistance under field conditions.

Peanut stem rot, also known as white mold, poses a significant threat to peanut production. It is typically managed using fungicides and moderately resistant cultivars. Cultivars with higher resistance can reduce fungicide dependency and increase sustainability. This study explores the potential of wild peanut species in stem rot resistance breeding programs by enhancing genetic diversity in cultivated peanut. Through greenhouse and field evaluations, 13 allotetraploid hybrids with Arachis stenosperma as one of the parents showed superior resistance compared to other wild genotypes. The genomic regions that confer the stem rot resistance were further identified by genotyping and phenotyping an F₂ population derived from the allotetraploid ValSten1 (A. valida × A. stenosperma)^4× and A. hypogaea cv. TifGP-2. A linkage map was constructed from 1926 SNP markers. QTL analysis revealed both beneficial and deleterious loci, with two resistance-associated QTLs derived from A. stenosperma and four susceptibility loci, two from A. stenosperma and two from A. valida. This is the first study that evaluated peanut-compatible wild-derived allotetraploids for stem rot resistance and that identified wild-derived QTLs for resistance to this pathogen. The allotetraploid hybrid ValSten1, that has A. stenosperma as one of the parents, offers a resource for resistance breeding. Markers associated with resistance QTLs can facilitate introgression from ValSten1 into cultivated peanut varieties in future breeding efforts, potentially reducing reliance on chemical control measures.

SUMMARY: This study, the second in a three‐part series, shows how peanut's polyploid origin enabled rapid diversification and enhanced domestication potential. Building on the knowledge that cultivated peanut ( Arachis hypogaea ) originated from a narrow hybridization between Arachis duranensis and Arachis ipaënsis less than 10 000 years ago, we are confronted with a paradox: how did such a narrow origin give rise to so much diversity—two subspecies, six botanical varieties, and thousands of landraces differing in growth habit, seed size, and pod morphology? Although several diploid Arachis species were cultivated earlier, only the allotetraploid became fully domesticated and widely adopted. The global success of peanut, despite its narrow genetic origin, suggests that polyploidization itself facilitated domestication. To test this hypothesis, we investigated how the two diploid progenitors and neoallotetraploids derived from a single hybridization and polyploidization event responded under artificial selection. In a pollinator‐free greenhouse, we advanced lineages of the neoallotetraploid and its diploid parents over 6 years, selecting for divergent seed weights. The neoallotetraploid showed a much stronger response to artificial selection than its diploid parents, while also spontaneously generating diverse phenotypic variation—including flower color, pod reticulation, and chlorophyll content—traits that distinguish A. hypogaea subspecies and landraces. These traits mirrored directional shifts in parental genome dosage caused by homoeologous exchange, supporting a causal connection with phenotype. These findings offer a compelling rationale for a domestication advantage in polyploid peanut, and provide a living demonstration of how a single ancestral tetraploid, despite an extreme genetic bottleneck, generates a phenotypic boom.

SUMMARY: This study, the third in a three‐part series, investigates whether chromosomal instability persists in cultivated peanut. The allotetraploid peanut ( Arachis hypogaea ; genome type AABB) originated from the hybridization and polyploidization of A. duranensis (AA) and A. ipaënsis (BB). Our first study established that this was an extremely narrow genetic origin, likely from a single hybridization event. This raised a paradox: how did such narrow genetics give rise to the phenotypic diversity seen in cultivated peanut? The second study addressed this, showing that a single neoallotetraploid spontaneously generates striking diversity, and that homoeologous exchanges—abundant in early generations following polyploidy—are a key mechanism in creating this diversity. In contrast to this early‐generation instability, cultivated peanut is generally considered to be genetically stable, presumably due to selection. This third study tests whether residual instability still occurs in modern peanut. From a single plant of the highly selfed ‘genome stock’ of the cultivar ‘Tifrunner’, we advanced lineages through seven generations in a pollinator‐free greenhouse. Among 233 plants, we identified three new large‐scale chromosomal instability events: a large deletion on chromosome B01, associated with reduced pod width and seed weight, and two ABBB compositions involving chromosomes A02/B02 and A05/B05. With these observations in hand, we reinterpreted previously published data from two recombinant inbred populations. Together, these results indicate that at least 1% of pure pedigree A. hypogaea plants exhibit spontaneous large‐scale chromosomal changes—a surprising frequency of instability that likely contributes to peanut's long‐term adaptability and evolution.

The Runner-type peanut (Arachis hypogaea L.) cultivar “Tifguard” carries an introgressed chromosomal segment on chromosome A09 from A. cardenasii that confers resistance to root-knot nematode (RKN). Despite this, a proportion of “Tifguard” plants show RKN symptoms, which could plausibly be attributed to seed mixture or outcrossing. However, recent work has shown that cultivated peanut exhibits surprisingly frequent large-scale chromosomal instability (1% to 5%); suggesting that resistance loss could arise from spontaneous structural genomic change. To test these possibilities, we grew foundation seed in an RKN-infested field and collected symptomatic and asymptomatic plants. Lineages derived by single-seed descent were genotyped using the Axiom Arachis 48K SNP array v2 and whole-genome sequencing. Symptomatic lineages lacked the A. cardenasii introgression on chromosome A09 and instead carried the complete endogenous A. hypogaea A09 region at the expected dosage. There was no evidence of large-scale homoeologous exchange, deletion, or other genomic instability affecting this chromosome. Most susceptible plants were closely related to resistant “Tifguard” but lacked the A09 introgression, with a smaller proportion assignable to known nematode-susceptible cultivars, implicating seed mixture with a possible contribution from cross-pollination rather than genomic instability. Because resistance depends on a single major-effect segment, rare events have disproportionate phenotypic impact, placing high demands on genetic purity. For important traits conferred by major loci, marker-based testing across seed-increase stages could verify trait retention directly, and is increasingly practical as marker costs decline.