Relationships of the wild peanut species, section Arachis: A resource for botanical classification, crop improvement, and germplasm management.

PREMISE: Wild species are strategic sources of valuable traits to be introduced into crops through hybridization. For peanut, the 33 currently described wild species in the section Arachis are particularly important because of their sexual compatibility with the domesticated species, Arachis hypogaea. Although numerous wild accessions are carefully preserved in seed banks, their morphological similarities pose challenges to routine classification. METHODS: Using a high-density array, we genotyped 272 accessions encompassing all diploid species in section Arachis. Detailed relationships between accessions and species were revealed through phylogenetic analyses and interpreted using the expertise of germplasm collectors and curators. RESULTS: Two main groups were identified: one with A genome species and the other with B, D, F, G, and K genomes. Species groupings generally showed clear boundaries. Structure within groups was informative, for instance, revealing the history of the proto-domesticate A. stenosperma. However, some groupings suggested multiple sibling species. Others were polyphyletic, indicating the need for taxonomic revision. Annual species were better defined than perennial ones, revealing limitations in applying classical and phylogenetic species concepts to the genus. We suggest new species assignments for several accessions. CONCLUSIONS: Curated by germplasm collectors and curators, this analysis of species relationships lays the foundation for future species descriptions, classification of unknown accessions, and germplasm use for peanut improvement. It supports the conservation and curation of current germplasm, both critical tasks considering the threats to the genus posed by habitat loss and the current restrictions on new collections and germplasm transfer.

Illegitimate Recombination between Duplicated Genes Generated from Recursive Polyploidizations Accelerated the Divergence of the Genus Arachis.

The peanut (Arachis hypogaea L.) is the leading oil and food crop among the legume family. Extensive duplicate gene pairs generated from recursive polyploidizations with high sequence similarity could result from gene conversion, caused by illegitimate DNA recombination. Here, through synteny-based comparisons of two diploid and three tetraploid peanut genomes, we identified the duplicated genes generated from legume common tetraploidy (LCT) and peanut recent allo-tetraploidy (PRT) within genomes. In each peanut genome (or subgenomes), we inferred that 6.8-13.1% of LCT-related and 11.3-16.5% of PRT-related duplicates were affected by gene conversion, in which the LCT-related duplicates were the most affected by partial gene conversion, whereas the PRT-related duplicates were the most affected by whole gene conversion. Notably, we observed the conversion between duplicates as the long-lasting contribution of polyploidizations accelerated the divergence of different Arachis genomes. Moreover, we found that the converted duplicates are unevenly distributed across the chromosomes and are more often near the ends of the chromosomes in each genome. We also confirmed that well-preserved homoeologous chromosome regions may facilitate duplicates' conversion. In addition, we found that these biological functions contain a higher number of preferentially converted genes, such as catalytic activity-related genes. We identified specific domains that are involved in converted genes, implying that conversions are associated with important traits of peanut growth and development.

A novel method for peanut variety identification and classification by Improved VGG16.

Crop variety identification is an essential link in seed detection, phenotype collection and scientific breeding. This paper takes peanut as an example to explore a new method for crop variety identification. Peanut is a crucial oil crop and cash crop. The yield and quality of different peanut varieties are different, so it is necessary to identify and classify different peanut varieties. The traditional image processing method of peanut variety identification needs to extract many features, which has defects such as intense subjectivity and insufficient generalization ability. Based on the deep learning technology, this paper improved the deep convolutional neural network VGG16 and applied the improved VGG16 to the identification and classification task of 12 varieties of peanuts. Firstly, the peanut pod images of 12 varieties obtained by the scanner were preprocessed with gray-scale, binarization, and ROI extraction to form a peanut pod data set with a total of 3365 images of 12 varieties. A series of improvements have been made to VGG16. Remove the F6 and F7 fully connected layers of VGG16. Add Conv6 and Global Average Pooling Layer. The three convolutional layers of conv5 have changed into Depth Concatenation and add the Batch Normalization(BN) layers to the model. Besides, fine-tuning is carried out based on the improved VGG16. We adjusted the location of the BN layers. Adjust the number of filters for Conv6. Finally, the improved VGG16 model's training test results were compared with the other classic models, AlexNet, VGG16, GoogLeNet, ResNet18, ResNet50, SqueezeNet, DenseNet201 and MobileNetv2 verify its superiority. The average accuracy of the improved VGG16 model on the peanut pods test set was 96.7%, which was 8.9% higher than that of VGG16, and 1.6-12.3% higher than that of other classical models. Besides, supplementary experiments were carried out to prove the robustness and generality of the improved VGG16. The improved VGG16 was applied to the identification and classification of seven corn grain varieties with the same method and an average accuracy of 90.1% was achieved. The experimental results show that the improved VGG16 proposed in this paper can identify and classify peanut pods of different varieties, proving the feasibility of a convolutional neural network in variety identification and classification. The model proposed in this experiment has a positive significance for exploring other Crop variety identification and classification.

Genetic diversity analysis of Korean peanut germplasm using 48 K SNPs 'Axiom_Arachis' Array and its application for cultivar differentiation.

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.

TMT-labeled quantitative proteomic analysis to identify proteins associated with the stability of peanut milk.

BACKGROUND: Peanut milk benefits human health mainly due to its high protein content and suitable amino acid composition. To reveal the molecular mechanism affecting the quality of peanut milk, tandem mass tag (TMT)-labeled proteomic analysis was applied to identify the proteome variation between two peanut cultivars that produced peanut milk with the best and worst stability. RESULTS: A total of 478 differentially abundant proteins (fold change >1.2 or <0.83, P < 0.05) were identified. Most of these proteins were located in the cytoplasm and chloroplasts. Correlation analysis showed that RNA recognition motif (RRM) domain-containing protein (17.1 kDa) had a negative relationship with the sedimentation rate of peanut milk and that 22.0 kDa class IV heat shock protein was negatively correlated with the creaming index (P < 0.05). Bioinformatic analysis showed that the molecular function of RRM domain-containing protein (17.1 kDa) was associated with RNA binding and nucleotide binding, and 22.0 kDa class IV heat shock protein was involved in the pathway of protein processing in the endoplasmic reticulum. CONCLUSION: Overall, the differentially abundant proteins in the biological metabolic pathway might offer some potential markers to guide future peanut breeding, especially for the production of peanut milk. © 2021 Society of Chemical Industry.

Genome-wide identification of meiotic recombination hot spots detected by SLAF in peanut (Arachis hypogaea L.).

Recombination hot spots (RHP), caused by meiosis, are considered to play crucial roles in improvement and domestication of crop. Cultivated peanut is one of the most important rich-source of oil and protein crops. However, no direct scale of recombination events and RHP have been estimated for peanut. To examine the scale of recombination events and RHP in peanut, a RIL population with 200 lines and a natural population with 49 cultivars were evaluated. The precise integrated map comprises 4837 SLAF markers with genetic length of 2915.46 cM and density of 1.66 markers per cM in whole genome. An average of 30.0 crossover (2.06 cMMb-1) events was detected per RIL plant. The crossover events (CE) showed uneven distribution among B sub-genome (2.32) and A sub-genome (1.85). There were 4.34% and 7.86% of the genome contained large numbers of CE (> 50 cMMb-1) along chromosomes in F6 and natural population, respectively. High density of CE regions called RHP, showed negative relationship to marker haplotypes conservative region but positive to heatmap of recombination. The genes located within the RHP regions by GO categories showed the responding of environmental stimuli, which suggested that recombination plays a crucial role in peanut adaptation to changing environments.

Presence of resveratrol in wild Arachis species adds new value to this overlooked genetic resource.

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.

Raman Spectroscopy Enables Non-Invasive Identification of Peanut Genotypes and Value-Added Traits.

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.

Origin traceability of peanut kernels based on multi-element fingerprinting combined with multivariate data analysis.

BACKGROUND: Multi-elements have been widely used to identify the geographical origins of various agricultural products. The objective of this study was to investigate the feasibility of identifying the geographical origins of peanut kernels at different regional scales by using the multi-element fingerprinting technique. The concentrations of 20 elements [boron (B), magnesium (Mg), phosphorus (P), potassium (K), calcium (Ca), etc.] were determined in 135 peanut samples from Jilin Province, Jiangsu Province, and Shandong Province of China. Data obtained were processed by one-way analysis of variance (ANOVA), principal components analysis (PCA), k nearest neighbors (k-NN), linear discriminant analysis (LDA), and support vector machine (SVM). RESULTS: Peanut kernels from different regions had their own element fingerprints. The k-NN, LDA, and SVM were all suitable to predict peanut kernels according to their grown provinces with the total correct classification rates of 91.2%, 91.1%, and 91.1%, respectively. While SVM was the best to identify different grown cities of peanut kernels with the prediction accuracy of 91.3%, compared to 72.2% and 78.3% for k-NN and LDA, respectively. CONCLUSION: It was an effective method to identify producing areas of peanut kernels at different regional scales using multi-element fingerprinting combined with SVM to enhance regional capabilities for quality assurance and control. © 2020 Society of Chemical Industry.

Genome-Wide Analysis of the Growth-Regulating Factor Family in Peanut (Arachis hypogaea L.).

Growth-regulating factors (GRFs) are plant-specific transcription factors that perform important functions in plant growth and development. Herein, we identified and characterised 24 AhGRF genes in peanut (Arachis hypogaea). AhGRF family genes were divided into six classes with OLQ and WRC domains. Transcriptome expression profile showed that more AhGRF genes, such as AhGRF5a gene, were at higher expression during pod development in Arachis monticola than cultivated species, especially at the pod rapid-expansion stage. AhGRF5a and AhGRF5b genes expressed at higher levels in pods than roots, leaves and stems tissues, existing in the difference between Arachis monticola and H8107. Exogenous GA3 application can activate AhGRF5a and AhGRF5b genes and H8107 line showed more positive response than Arachis monticola species. These results imply that these two AhGRF genes may be active during the peanut pod development.

Transcriptomic Analysis Reveals the High-Oleic Acid Feedback Regulating the Homologous Gene Expression of Stearoyl-ACP Desaturase 2 (SAD2) in Peanuts.

Peanuts with high oleic acid content are usually considered to be beneficial for human health and edible oil storage. In breeding practice, peanut lines with high monounsaturated fatty acids are selected using fatty acid desaturase 2 (FAD2), which is responsible for the conversion of oleic acid (C18:1) to linoleic acid (C18:2). Here, comparative transcriptomics were used to analyze the global gene expression profile of high- and normal-oleic peanut cultivars at six time points during seed development. First, the mutant type of FAD2 was determined in the high-oleic peanut (H176). The result suggested that early translation termination occurred simultaneously in the coding sequence of FAD2-A and FAD2-B, and the cultivar H176 is capable of utilizing a potential germplasm resource for future high-oleic peanut breeding. Furthermore, transcriptomic analysis identified 74 differentially expressed genes (DEGs) involved in lipid metabolism in high-oleic peanut seed, of which five DEGs encoded the fatty acid desaturase. Aradu.XM2MR belonged to the homologous gene of stearoyl-ACP (acyl carrier protein) desaturase 2 (SAD2) that converted the C18:0 into C18:1. Further subcellular localization studies indicated that FAD2 was located at the endoplasmic reticulum (ER), and Aradu.XM2MR was targeted to the plastid in Arabidopsis protoplast cells. To examine the dynamic mechanism of this finding, we focused on the peroxidase (POD)-mediated fatty acid (FA) degradation pathway. The fad2 mutant significantly increased the POD activity and H2O2 concentration at the early stage of seed development, implying that redox signaling likely acted as a messenger to connect the signaling transduction between the high-oleic content and Aradu.XM2MR transcription level. Taken together, transcriptome analysis revealed the feedback mechanism of SAD2 (Aradu.XM2MR) associated with FAD2 mutation during the seed developmental stage, which could provide a potential peanut breeding strategy based on identified candidate genes to improve the content of oleic acid.

Sensory Characterization of Dominant Malawi Peanut Varieties After Roasting.

Although sensory appeal influences peanut consumption, peanut varieties are mostly selected based on agronomic traits. As a result, the sensory properties of peanut varieties, especially in southern Africa, are not known. Therefore, the primary objective of the study was to determine the sensory properties of the Malawi peanut varieties and the volatile compounds associated with roasted peanut flavor. Six dominant Malawi peanut varieties (Chalimbana, CG7, Nsinjiro, Kakoma, Baka, and Chitala) were evaluated in this study. All peanut samples were shelled and then, roasted in a convection oven to reach medium doneness as indicated by the surface color lightness (L) value of approximately 50. A hybrid descriptive analysis (DA) was done to determine the sensory profile of the roasted peanuts. Volatile compounds were extracted from equilibrated ground peanut sample using headspace-solid phase microextraction technique and analyzed by GC-MS. Analysis of Variance (ANOVA) of the DA data showed significant differences (P < 0.05) in the sensory profiles of the peanut varieties. Nsinjiro and Baka had a significantly higher intensity of roasted peanutty aroma and flavor (P < 0.05). The GC-MS results showed that pyrazines and furans were the dominant volatile compounds but, their respective concentrations, in the evaluated peanut varieties, were significantly different (P < 0.05). Among the pyrazines, 2-ethyl-3,5-dimethyl pyrazine was strongly correlated with roasted peanutty flavor (r = 0.927) just like 2,5 dimethyl pyrazine (r = 0.916). Therefore, 2-ethyl-3,5-dimethyl pyrazine and 2,5-dimethyl pyrazine production pathways could provide more insights into the origins of roasted peanut flavor. PRACTICAL APPLICATION: The findings of this study can help food product developers, who have no access to sensory and analytical analyses, to identify Malawi peanut varieties that are suitable for various food applications. Furthermore, plant breeders could also use the findings to inform new projects aimed at improving the sensory properties of the peanut varieties.

Selected nutrients and antinutrients in peanut cultivars harvested in Brazil.

BACKGROUND: There are more than 30 peanut cultivars registered in Brazil. However, there are no published data about the content of nutrients and antinutrients even in the most commercially important ones. Therefore, our objective was to characterize commercial peanut cultivars harvested in Brazil by determining proximate and fatty acid composition and content of selected minerals and phytates, saponins and condensed tannins. RESULTS: Significant variations were found among the cultivars for almost all studied nutrients, except Mg. Granoleico and IAC 505 were identified as high oleic. Results were compared with data from the Brazilian Food Composition Table (TACO) and, for this, percentage differences (D%) were calculated. Appreciable D% were found for proteins, lipids, ash, dietary fiber, almost all fatty acids (except 20:0) and almost all studied minerals (except zinc). Moreover, remarkable variations in content of antinutrients were observed. IAC Red Tatu had the highest content of saponins; IAC OL3 and IAC 886 had the highest amounts of phytates; and IAC 886 had the highest amounts of condensed tannins. CONCLUSION: Results confirm the relevance of differentiating cultivars in the market and in national food composition tables and databases. Furthermore, some of these cultivars may be indicated for new use trends. © 2019 Society of Chemical Industry.

The genome sequence of segmental allotetraploid peanut Arachis hypogaea.

Like many other crops, the cultivated peanut (Arachis hypogaea L.) is of hybrid origin and has a polyploid genome that contains essentially complete sets of chromosomes from two ancestral species. Here we report the genome sequence of peanut and show that after its polyploid origin, the genome has evolved through mobile-element activity, deletions and by the flow of genetic information between corresponding ancestral chromosomes (that is, homeologous recombination). Uniformity of patterns of homeologous recombination at the ends of chromosomes favors a single origin for cultivated peanut and its wild counterpart A. monticola. However, through much of the genome, homeologous recombination has created diversity. Using new polyploid hybrids made from the ancestral species, we show how this can generate phenotypic changes such as spontaneous changes in the color of the flowers. We suggest that diversity generated by these genetic mechanisms helped to favor the domestication of the polyploid A. hypogaea over other diploid Arachis species cultivated by humans.

Identification and characterization of aquaporin genes in Arachis duranensis and Arachis ipaensis genomes, the diploid progenitors of peanut.

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.

Effect of Physiochemical Factors and Peanut Varieties on the Charge Stability of Oil Bodies Extracted by Aqueous Method.

In order to explore the scientific basis for the application of oil bodies (OBs) from different peanut varieties in food, the effect of NaCl (0-100 mM), thermal processing (25-45°C, 1 h) and pH (3.0, 7.4, and 9.0) on their zeta potentials was analyzed in this study. The zeta potentials of OB suspensions (in 10 mM phosphate buffer) prepared from five peanut varieties in different salt concentrations (0-100 mM) were positive at pH 3.0, while they remained negative at pH 7.4 and 9.0. The absolute values of zeta potentials were over 20 mV at a lower salt concentration (< 10 mM NaCl) at pH 3.0 and 7.4. Particularly, the values of zeta potentials of Yuhua27 and Yuhua9830 were as high as 40 mV in the absence of NaCl at pH 7.4. The OBs exhibited diverse change trends between the five peanut varieties in the temperatures from 25 to 45°C (0 mM NaCl, pH 7.4). The OBs from Yuhua9830 exhibited the best thermal adaptability at the different temperatures tested than the other four peanut varieties. These outcomes suggested that OBs extracted from different varieties possess diverse properties and may provide a new insight into choosing a suitable peanut variety for the food industry.

Effect of Planting Date and Peanut Cultivar on Epidemics of Late Leaf Spot in Georgia.

Field trials were conducted in 2015 and 2016 in Tifton, GA to determine the effects of planting dates (24 and 27 April, 4, 11, 19, and 26 May 2015; and 11, 18, and 25 April and 2, 9, and 16 May 2016), peanut (Arachis hypogaea) cultivar (Georgia-06G and Georgia-12Y), and seed treatment (nontreated and treated with azoxystrobin, fludioxonil, and mefenoxam) on epidemics of late leaf spot (Nothopassalora personata), plant populations, and peanut yield. Final severity and AUDPC of late leaf spot increased with later planting dates in both years. For most planting dates in 2015 and the final planting date in 2016, final leaf spot severity and AUDPC were lower for Georgia-12Y than for Georgia-06G. Seed treatment increased plant populations for the 27 April and 4 May planting dates in 2015 and across all other treatments in 2016. Yields were higher for Georgia-12Y than for Georgia-06G in both years. In 2015, yields of both cultivars decreased according to linear functions of day of year of planting date, but there was no effect of planting date on yield in 2016. The combination of early planting with Georgia-12Y shows potential utility for management of leaf spot in situations such as organic production where fungicide use is minimal.

Image features and DUS testing traits for peanut pod variety identification and pedigree analysis.

BACKGROUND: DUS (Distinctness, Uniformity and Stability) testing of new varieties is an important method for peanut germplasm evaluation and identification of varieties. In order to verify the feasibility of variety identification for peanut DUS testing based on image processing, 2000 peanut pod images from 20 varieties were obtained by a scanner. Initially, six DUS testing traits were quantified using a mathematical method based on image processing technology, and then, size, shape, color and texture features (total 31) were also extracted. Next, the Fisher algorithm was used as a feature selection method to select 'good' features from the extracted features to expand the DUS testing traits set. Finally, support vector machine (SVM) and K-means algorithm were respectively used as recognition model and clustering method for variety identification and pedigree clustering. RESULTS: By the Fisher selection method, a number of significant candidate features for DUS testing were selected which can be used in the DUS testing further; using the top half of these features (about 18) ordered by Fisher discrimination ability, the recognition rate of SVM model was found to be more than 90%, which was better than unordered features. In addition, a pedigree clustering tree of 20 peanut varieties was built based on the K-means clustering method, which can be used in deeper studies of the genetic relationship of different varieties. CONCLUSION: This article can provide a novel reference method for future DUS testing, peanut varieties identification and study of peanut pedigree. © 2018 Society of Chemical Industry.

Genetic Diversity, Population Structure, and Botanical Variety of 320 Global Peanut Accessions Revealed Through Tunable Genotyping-by-Sequencing.

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 (FST) value confirmed that var. fastigiata and var. vulgaris were closely related to each other (FST = 0.284), while both of them were clearly distinct from var. hypogaea (FST > 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.

SNP genotyping reveals major QTLs for plant architectural traits between A-genome peanut wild species.

KEY MESSAGE: QTL mapping of important architectural traits was successfully applied to an A-genome diploid population using gene-specific variations. Peanut wild species are an important source of resistance to biotic and possibly abiotic stress; because these species differ from the cultigen in many traits, we have undertaken to identify QTLs for several plant architecture-related traits. In this study, we took recently identified SNPs, converted them into markers, and identified QTLs for architectural traits. SNPs from RNASeq data distinguishing two parents, A. duranensis (KSSc38901) and A. cardenasii (GKP10017), of a mapping population were identified using three references-A. duranensis V14167 genome sequence, and transcriptome sequences of A. duranensis KSSc38901 and OLin. More than 49,000 SNPs differentiated the parents, and 87.9% of the 190 SNP calls tested were validated. SNPs were then genotyped on 91 F2 lines using KASP chemistry on a Roche LightCycler 480 and a Fluidigm Biomark HD, and using SNPType chemistry on the Fluidigm Biomark HD. A linkage map was constructed having ten linkage groups, with 144 loci spanning a total map distance of 1040 cM. Comparison of the A-genome map to the A. duranensis genome sequence revealed a high degree of synteny. QTL analysis was also performed on the mapping population for important architectural traits. Fifteen definitive and 16 putative QTLs for petiole length, leaflet length and width, leaflet area, leaflet length/width ratio, main stem height, presence of flowers on the main stem, and seed mass were identified. Results demonstrate that SNPs identified from transcriptome sequencing could be converted to KASP or SNPType markers with a high success rate, and used to identify alleles with significant phenotypic effects, These could serve as information useful for introgression of alleles into cultivated peanut from wild species and have the potential to allow breeders to more easily fix these alleles using a marker-assisted backcrossing approach.