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• Background and Aims The genus Arachis contains 80 described species. Section Arachis is of particular interest because it includes cultivated peanut, an allotetraploid, and closely related wild species, most of which are diploids. This study aimed to analyse the genetic relationships of multiple accessions of section Arachis species using two complementary methods. Microsatellites allowed the analysis of inter- and intraspecific variability. Intron sequences from single-copy genes allowed phylogenetic analysis including the separation of the allotetraploid genome components. • Methods Intron sequences and microsatellite markers were used to reconstruct phylogenetic relationships in section Arachis through maximum parsimony and genetic distance analyses. • Key Results Although high intraspecific variability was evident, there was good support for most species.However, some problems were revealed, notably a probable polyphyletic origin for A. kuhlmannii. The validity of the genome groups was well supported. The F, K and D genomes grouped close to the A genome group. The 2n = 18 species grouped closer to the B genome group. The phylogenetic tree based on the intron data strongly indicated that A. duranensis and A. ipaënsis are the ancestors of A. hypogaea and A. montícola. Intron nucleotide substitutions allowed the ages of divergences of the main genome groups to be estimated at a relatively recent 2.3-2.9 million years ago. This age and the number of species described indicate a much higher speciation rate for section Arachis than for legumes in general. • Conclusions The analyses revealed relationships between the species and genome groups and showed a generally high level of intraspecific genetic diversity. The improved knowledge of species relationships should facilitate the utilization of wild species for peanut improvement. The estimates of speciation rates in section Arachis are high, but not unprecedented. We suggest these high rates may be linked to the peculiar reproductive biology of Arachis.

Background Aquaporins (AQPs) facilitate transport of water and small solutes across cell membranes and play an important role in different physiological processes in plants. Despite their importance, limited data is available about AQP distribution and function in the economically important oilseed crop peanut, Arachis hypogea (AABB). The present study reports the identification and structural and expression analysis of the AQPs found in the diploid progenitor genomes of A. hypogea i.e. Arachis duranensis (AA) and Arachis ipaensis (BB). Results Genome-wide analysis revealed the presence of 32 and 36 AQPs in A. duranensis and A. ipaensis , respectively. Phylogenetic analysis showed similar numbers of AQPs clustered in five distinct subfamilies including the plasma membrane intrinsic proteins (PIPs), the tonoplast intrinsic proteins (TIPs), the nodulin 26-like intrinsic proteins (NIPs), the small basic intrinsic proteins (SIPs), and the uncharacterized intrinsic proteins (XIPs). A notable exception was the XIP subfamily where XIP1 group was observed only in A. ipaensis genome. Protein structure evaluation showed a hydrophilic aromatic/arginine (ar/R) selectivity filter (SF) in PIPs whereas other subfamilies mostly contained a hydrophobic ar/R SF. Both genomes contained one NIP2 with a GSGR SF indicating a conserved ability within the genus to uptake silicon. Analysis of RNA-seq data from A. hypogea revealed a similar expression pattern for the different AQP paralogs of AA and BB genomes. The TIP3s showed seed-specific expression while the NIP1s’ expression was confined to roots and root nodules. Conclusions The identification and the phylogenetic analysis of AQPs in both Arachis species revealed the presence of all five sub-families of AQPs. Within the NIP subfamily, the presence of a NIP2 in both genomes supports a conserved ability to absorb Si within plants of the genus. The global expression profile of AQPs in A. hypogea revealed a similar pattern of AQP expression regardless of the subfamilies or the genomes. The tissue-specific expression of AQPs suggests an important role in the development and function of the respective organs. The AQPs identified in the present study will serve as a resource for further characterization and possible exploitation of AQPs to understand their physiological role in A. hypogea .

Identification of specific genotypes can be accomplished by visual recognition of their distinct phenotypical appearance, as well as DNA analysis. Visual identification (ID) of species is subjective and usually requires substantial taxonomic expertise. Genotyping and sequencing are destructive, time- and labor-consuming. In this study, we investigate the potential use of Raman spectroscopy (RS) as a label-free, non-invasive and non-destructive analytical technique for the fast and accurate identification of peanut genotypes. We show that chemometric analysis of peanut leaflet spectra provides accurate identification of different varieties. This same analysis can be used for prediction of nematode resistance and oleic-linoleic oil (O/L) ratio. Raman-based analysis of seeds provides accurate genotype identification in 95% of samples. Additionally, we present data on the identification of carbohydrates, proteins, fiber and other nutrients obtained from spectroscopic signatures of peanut seeds. These results demonstrate that RS allows for fast, accurate and non-invasive screening and selection of plants which can be used for precision breeding.

Absract Peanut ( Arachis hypogaea L .) is an important oilseed and cash crop worldwide. Wild Arachis spp. are potental sources of novel genes for the genetic improvement of cultivated peanut. Understanding the genetic relationships with cultivated peanut is important for the efficient use of wild species in breeding programmes. However, for this genus, only a few genetic resources have been explored so far. In this study, new chloroplast genomic resources have been developed for the genus Arachis based on whole chloroplast genomes from seven species that were sequenced using next-generation sequencing technologies. The chloroplast genomes ranged in length from 156,275 to 156,395 bp, and their gene contents, gene orders, and GC contents were similar to those for other Fabaceae species. Comparative analyses among the seven chloroplast genomes revealed 643 variable sites that included 212 singletons and 431 parsimony-informative sites. We also identified 101 SSR loci and 85 indel mutation events. Thirty-seven SSR loci were found to be polymorphic by in silico comparative analyses. Eleven highly divergent DNA regions, suitable for phylogenetic and species identification, were detected in the seven chloroplast genomes. A molecular phylogeny based on the complete chloroplast genome sequences provided the best resolution of the seven Arachis species.

Genus Arachis comprises 82 species distributed into nine taxonomic sections. Most Arachis species are wild and those from Arachis section have been evaluated for many traits, since they can be used in peanut breeding. Most of the remaining species have been neglected and understudied. Recently, resveratrol content and expression of a resveratrol synthase gene were analyzed in wild Arachis species. Our aim was to expand the knowledge about resveratrol in Arachis , analyzing species from five sections and evaluating the expression of a resveratrol synthase (RS) gene responsive to ultraviolet light (UV) along the time. In a first experiment, the resveratrol content after UV induction was analyzed on detached leaves of 12 species from five sections. Variation was observed among species and accessions of the same species. The highest contents were found in A. lignosa (843.9 μg/g) and A. triseminata (745.4 μg/g) . In a second experiment, RS expression and resveratrol content in four species and one synthetic amphidiploid were analyzed at 0, 7, 15 and 24 h pos induction (hpi) with UV. In most genotypes, the highest RS expression level was at 0 hpi, whereas the highest resveratrol content was at 15 hpi. Our results suggested that resveratrol is ubiquitously present in the genus Arachis with different capacities of synthesis among species and accessions in response to ultraviolet treatment. Presence of resveratrol in wild Arachis species adds new value to these genetic resources.

Cultivated peanut ( Arachis hypogaea L.) were classified into six botanical varieties according to the morphological characteristics. However, their genetic evolutionary relationships at the genome-wide level were still unclear. A total of 320 peanut accessions, including four of the six botanical varieties, and 37,128 high-quality single nucleotide polymorphisms (SNPs) detected by tunable genotyping-by-sequencing (tGBS) were used to reveal the evolutionary relationships among different botanical varieties and verify the phenotypic classification. A phylogenetic tree indicated that the tested accessions were grouped into three clusters. Almost all of the peanut accessions in cluster C1 belong to var. fastigiata , and clusters C2 and C3 mainly consisted of accessions from var. vulgaris and subsp. hypogaea , respectively. The results of a principal component analysis were consistent with relationships revealed in the phylogenetic tree. Population structure analysis showed that var. fastigiata and var. vulgaris were not separated when K = 2 (subgroup number), whereas they were clearly divided when K = 3. However, var. hypogaea and var. hirsuta could not be distinguished from each other all the way. The nucleotide diversity (π) value implied that var. vulgaris exhibited the highest genetic diversity (0.048), followed by var. fastigiata (0.035) and subsp. hypogaea (0.012), which is consistent with the result of phylogenetic tree. Moreover, the fixation index ( F ST ) value confirmed that var. fastigiata and var. vulgaris were closely related to each other ( F ST  = 0.284), while both of them were clearly distinct from var. hypogaea ( F ST  > 0.4). The present study confirmed the traditional botanical classifications of cultivated peanut at the genome-wide level. Furthermore, the reliable SNPs identified in this study may be a valuable resource for peanut breeders.

Peanut, Arachis hypogaea L., is a protein-rich species consumed worldwide. A key improvement to peanut culture involves the development of cultivars that resist fungal diseases such as rust, leaf spot and scab. Over three years, we evaluated fungal resistance under field conditions of 43 wild accessions and three interspecific hybrids of the genus Arachis, as well as six A. hypogaea genotypes. In the first year, we evaluated resistance to early and late leaf spot, rust and scab. In the second and third years, we evaluated the 18 wild species with the best resistance scores and control cultivar IAC Caiapó for resistance to leaf spot and rust. All wild accessions displayed greater resistance than A. hypogaea but differed in their degree of resistance, even within the same species. We found accessions with as good as or better resistance than A. cardenasii, including: A. stenosperma (V15076 and Sv 3712), A. kuhlmannii (V 6413), A. kempff-mercadoi (V 13250), A. hoehnei (KG 30006), and A. helodes (V 6325). Amphidiploids and hybrids of A. hypogaea behaved similarly to wild species. An additional four accessions deserve further evaluation: A. magna (V 13751 and KG 30097) and A. gregoryi (V 14767 and V 14957). Although they did not display as strong resistance as the accessions cited above, they belong to the B genome type that is crucial to resistance gene introgression and pyramidization in A. hypogaea.

Cultivated peanut ( Arachis hypogaea ) is one of the important legume oilseed crops. Cultivated peanut has a narrow genetic base. Therefore, it is necessary to widen its genetic base and diversity for additional use. The objective of the present study was to assess the genetic diversity and population structure of 96 peanut genotypes with 9478 high-resolution SNPs identified from a 48 K ‘Axiom_Arachis’ SNP array. Korean set genotypes were also compared with a mini-core of US genotypes. These sets of genotypes were used for genetic diversity analysis. Model-based structure analysis at K = 2 indicated the presence of two subpopulations in both sets of genotypes. Phylogenetic and PCA analysis clustered these genotypes into two major groups. However, clear genotype distribution was not observed for categories of subspecies, botanical variety, or origin. The analysis also revealed that current Korean genetic resources lacked variability compared to US mini-core genotypes. These results suggest that Korean genetic resources need to be expanded by creating new allele combinations and widening the genetic pool to offer new genetic variations for Korean peanut improvement programs. High-quality SNP data generated in this study could be used for identifying varietal contaminant, QTL, and genes associated with desirable traits by performing mapping, genome-wide association studies.

Effective weed detection for precise management remains a pertinent issue in modern agriculture. In this study, hyperspectral imaging (HSI) was combined with machine learning (ML) to differentiate between peanut plants and four common weeds found in peanut fields. Several spectral preprocessing methods—Moving Window Averaging (MWA), Median Filtering (MF), Gaussian Filtering (GF), and Savitzky–Golay smoothing (SGS)—were applied. Feature selection algorithms, including Correlation-based feature selection (CFS), Principal Components Analysis (PCA), and Wrapper Feature Selection (WFS), were then used to extract the most informative wavelengths. Among the various classifiers evaluated, the combination of MF preprocessing, WFS algorithm, and LDA classifier (MF-WFS-LDA) achieved the best performance, while the WFS method selected 12 optimal wavelengths from a total of 465. The accuracy, precision, recall, and RMSE values of this model in the training stage were 99.71%, 0.997, 0.997, and 0.054, respectively. These statistics were 96.67%, 0.967, 0.968, and 0.088, respectively, in the test stage. Furthermore, it successfully differentiated peanuts from each weed species using a minimal number of optimal wavelengths. These findings highlight the potential of integrating HSI with ML for precise weed detection in peanut cultivation. However, further validation under diverse environmental and field conditions is recommended.

Cultivated peanut possesses an extremely narrow genetic basis. Polymorphism is considerably difficult to identify with the use of conventional biochemical and molecular tools. For the purpose of obtaining considerable DNA polymorphisms and fingerprinting cultivated peanut genotypes in a convenient manner, start codon targeted polymorphism technique was used to study genetic diversity and relatedness among 20 accessions of four major botanical varieties of peanut. Of 36 primers screened, 18 primers could produce unambiguous and reproducible bands. All 18 primers generated a total of 157 fragments, with a mean of 8.72 ranging from 4 to 17 per primer. Of 157 bands, 60 (38.22%) were polymorphic. One to seven polymorphic bands were amplified per primer, with 3.33 polymorphic bands on average. Polymorphism per primer ranged from 14.29 to 66.67%, with an average of 36.76%. The results revealed that not all accessions of the same variety were grouped together and high genetic similarity was detected among the tested genotypes based on cluster analysis and genetic distance analysis, respectively. Further, accession-specific markers were observed in several accessions. All these results demonstrated the following: (1) start codon targeted polymorphism technique can be utilized to identify DNA polymorphisms and fingerprint cultivars in domesticated peanut, and (2) it possesses considerable potential for studying genetic diversity and relationships among peanut accessions.