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Thrips (Enneothrips flavens) is a pest that causes severe damage and yield losses to peanut crop if not properly controlled. The main control method currently used by farmers is bi-weekly application of insecticides during crop development, which, in addition to its toxicity, is very costly. Thus, new sources of resistance must be identified in order to reduce the use of insecticides and effectively manage the pest. This study aimed to evaluate the occurrence and symptoms of E. flavens infestations in 12 accessions of 10 wild species of Arachis and nine amphidiploids, as well as to compare their morphoagronomic characteristics to those of commercial cultivars. To this end, we conducted experiments during two summer seasons, using a randomized block design with four replications. We conducted evaluations of the severity of infestation, noting visual symptoms of E. flavens and morphological and reproductive characteristics of the Arachis plants. Results indicated that wild accessions V 7635 (A. vallsii), V 13250 (A. kempff-mercadoi), K 9484 (A. batizocoi), Wi 1118 (A. williamsii), V 14167 (A. duranensis) and V 13751 (A. magna) are the most promising for obtaining useful new amphidiploids. Among the amphidiploids, An 12 (A. batizocoi x A. kempff-mercadoi)4x, An 9 (A. gregoryi x A. stenosperma) 4x, and An 8 (A. magna x A. cardenasii)4x showed high level of resistance to E. flavens. The identified thrips resistant wild and amphidiploid Arachis species may be used in future breeding program to produce thrips resistant peanut cultivars.

Peanut or groundnut (Arachis hypogaea L.), a legume of South American origin, has high seed oil content (45–56%) and is a staple crop in semiarid tropical and subtropical regions, partially because of drought tolerance conferred by its geocarpic reproductive strategy. We present a draft genome of the peanut A-genome progenitor, Arachis duranensis, and 50,324 protein-coding gene models. Patterns of gene duplication suggest the peanut lineage has been affected by at least three polyploidizations since the origin of eudicots. Resequencing of synthetic Arachis tetraploids reveals extensive gene conversion in only three seed-to-seed generations since their formation by human hands, indicating that this process begins virtually immediately following polyploid formation. Expansion of some specific gene families suggests roles in the unusual subterranean fructification of Arachis. For example, the S1Fa-like transcription factor family has 126 Arachis members, in contrast to no more than five members in other examined plant species, and is more highly expressed in roots and etiolated seedlings than green leaves. The A. duranensis genome provides a major source of candidate genes for fructification, oil biosynthesis, and allergens, expanding knowledge of understudied areas of plant biology and human health impacts of plants, informing peanut genetic improvement and aiding deeper sequencing of Arachis diversity.

Background WRKY proteins are important transcription factors (TFs) in plants, involved in growth and development and responses to environmental changes. Although WRKY TFs have been studied at the genome level in Arachis genus, including oil crop and turfgrass, their regulatory networks in controlling flowering time remain unclear. The aim of this study was to predict the molecular mechanisms of WRKY TFs regulation flowering time in Arachis genus at the genome level using bioinformatics approaches. Results The flowering-time genes of Arachis genus were retrieved from the flowering-time gene database. The regulatory networks between WRKY TFs and downstream genes in Arachis genus were predicted using bioinformatics tools. The results showed that WRKY TFs were involved in aging, autonomous, circadian clock, hormone, photoperiod, sugar, temperature, and vernalization pathways to modulate flowering time in Arachis duranensis , Arachis ipaensis , Arachis monticola , and Arachis hypogaea cv. Tifrunner. The WRKY TF binding sites in homologous flowering-time genes exhibited asymmetric evolutionary pattern, indicating that the WRKY TFs interact with other transcription factors to modulate flowering time in the four Arachis species. Protein interaction network analysis showed that WRKY TFs interacted with FRUITFULL and APETALA2 to modulate flowering time in the four Arachis species. WRKY TFs implicated in regulating flowering time had low expression levels, whereas their interaction proteins had varying expression patterns in 22 tissues of A. hypogaea cv. Tifrunner. These results indicate that WRKY TFs exhibit antagonistic or synergistic interactions with the associated proteins. Conclusions This study reveals complex regulatory networks through which WRKY TFs modulate flowering time in the four Arachis species using bioinformatics approaches.

High oil and protein content make tetraploid peanut a leading oil and food legume. Here we report a high-quality peanut genome sequence, comprising 2.54 Gb with 20 pseudomolecules and 83,709 protein-coding gene models. We characterize gene functional groups implicated in seed size evolution, seed oil content, disease resistance and symbiotic nitrogen fixation. The peanut B subgenome has more genes and general expression dominance, temporally associated with long-terminal-repeat expansion in the A subgenome that also raises questions about the A-genome progenitor. The polyploid genome provided insights into the evolution of Arachis hypogaea and other legume chromosomes. Resequencing of 52 accessions suggests that independent domestications formed peanut ecotypes. Whereas 0.42–0.47 million years ago (Ma) polyploidy constrained genetic variation, the peanut genome sequence aids mapping and candidate-gene discovery for traits such as seed size and color, foliar disease resistance and others, also providing a cornerstone for functional genomics and peanut improvement. High-quality genome sequence of cultivated peanut comprising 2.54 Gb with 20 pseudomolecules and 83,709 protein-coding gene models provides insights into genome evolution and the genetic mechanisms underlying seed size and leaf resistance in peanut.

KEY MESSAGE : Successful introgression of a major QTL for rust resistance, through marker-assisted backcrossing, in three popular Indian peanut cultivars generated several promising introgression lines with enhanced rust resistance and higher yield. Leaf rust, caused by Puccinia arachidis Speg, is one of the major devastating diseases in peanut (Arachis hypogaea L.). One QTL region on linkage group AhXV explaining upto 82.62 % phenotypic variation for rust resistance was validated and introgressed from cultivar ‘GPBD 4’ into three rust susceptible varieties (‘ICGV 91114’, ‘JL 24’ and ‘TAG 24’) through marker-assisted backcrossing (MABC). The MABC approach employed a total of four markers including one dominant (IPAHM103) and three co-dominant (GM2079, GM1536, GM2301) markers present in the QTL region. After 2–3 backcrosses and selfing, 200 introgression lines (ILs) were developed from all the three crosses. Field evaluation identified 81 ILs with improved rust resistance. Those ILs had significantly increased pod yields (56–96 %) in infested environments compared to the susceptible parents. Screening of selected 43 promising ILs with 13 markers present on linkage group AhXV showed introgression of the target QTL region from the resistant parent in 11 ILs. Multi-location field evaluation of these ILs should lead to the release of improved varieties. The linked markers may be used in improving rust resistance in peanut breeding programmes.

Globally, drought stress poses a significant threat to crop productivity. Improving the drought tolerance of crops with microbial biostimulants is a sustainable strategy to meet a growing population’s demands. This research aimed to elucidate microbial biostimulants’ (Plant Growth Promoting Rhizobacteria) role in alleviating drought stress in oil-seed crops. In total, 15 bacterial isolates were selected for drought tolerance and screened for plant growth-promoting (PGP) attributes like phosphate solubilization and production of indole-3-acetic acid, siderophore, hydrogen cyanide, ammonia, and exopolysaccharide. This research describes two PGPR strains: Acinetobacter calcoaceticus AC06 and Bacillus amyloliquefaciens BA01. The present study demonstrated that these strains (AC06 and BA01) produced abundant osmolytes under osmotic stress, including proline (2.21 and 1.75 µg ml − 1 ), salicylic acid (18.59 and 14.21 µg ml − 1 ), trehalose (28.35 and 22.74 µg mg − 1 FW) and glycine betaine (11.35 and 7.74 mg g − 1 ) respectively. AC06 and BA01 strains were further evaluated for their multifunctional performance by inoculating in Arachis hypogaea L. (Groundnut) under mild and severe drought regimes (60 and 40% Field Capacity). Inoculation with microbial biostimulants displayed distinct osmotic-adjustment abilities of the groundnut, such as growth parameters, plant biomass, photosynthetic pigments, relative water content, proline, and soluble sugar in respective to control during drought. On the other hand, plant sensitivity indexes such as electrolyte leakage and malondialdehyde (MDA) contents were decreased as well as cooperatively conferred plant drought tolerance by induced alterations in stress indicators such as catalase (CAT), ascorbate peroxidase (APX), and superoxide dismutase (SOD). Thus, Acinetobacter sp. AC06 and Bacillus sp. BA01 can be considered as osmolyte producing microbial biostimulants to simultaneously induce osmotic tolerance and metabolic changes in groundnuts under drought stress.

Background Peanut is one of the most important oil crop species worldwide. NAC transcription factor (TF) genes play important roles in the salt and drought stress responses of plants by activating or repressing target gene expression. However, little is known about NAC genes in peanut. Results We performed a genome-wide characterization of NAC genes from the diploid wild peanut species Arachis duranensis and Arachis ipaensis , which included analyses of chromosomal locations, gene structures, conserved motifs, expression patterns, and cis -acting elements within their promoter regions. In total, 81 and 79 NAC genes were identified from A. duranensis and A. ipaensis genomes. Phylogenetic analysis of peanut NACs along with their Arabidopsis and rice counterparts categorized these proteins into 18 distinct subgroups. Fifty-one orthologous gene pairs were identified, and 46 orthologues were found to be highly syntenic on the chromosomes of both A. duranensis and A. ipaensis . Comparative RNA sequencing (RNA-seq)-based analysis revealed that the expression of 43 NAC genes was up- or downregulated under salt stress and under drought stress. Among these genes, the expression of 17 genes in cultivated peanut ( Arachis hypogaea ) was up- or downregulated under both stresses. Moreover, quantitative reverse transcription PCR (RT-qPCR)-based analysis revealed that the expression of most of the randomly selected NAC genes tended to be consistent with the comparative RNA-seq results. Conclusion Our results facilitated the functional characterization of peanut NAC genes, and the genes involved in salt and drought stress responses identified in this study could be potential genes for peanut improvement.

• 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.

Key messageGenetic mapping identified large number of epistatic interactions indicating the complex genetic architecture for stem rot disease resistance.Groundnut (Arachis hypogaea) is an important global crop commodity and serves as a major source of cooking oil, diverse confectionery preparations and livestock feed. Stem rot disease caused by Sclerotium rolfsii is the most devastating disease of groundnut and can cause up to 100% yield loss. Genomic-assisted breeding (GAB) has potential for accelerated development of stem rot resistance varieties in short period with more precision. In this context, linkage analysis and quantitative trait locus (QTL) mapping for resistance to stem rot disease was performed in a bi-parental recombinant inbred line population developed from TG37A (susceptible) × NRCG-CS85 (resistant) comprising of 270 individuals. Genotyping-by-sequencing approach was deployed to generate single nucleotide polymorphism (SNP) genotyping data leading to development of a genetic map with 585 SNP loci spanning map distance of 2430 cM. QTL analysis using multi-season phenotyping and genotyping data could not detect any major main-effect QTL but identified 44 major epistatic QTLs with phenotypic variation explained ranging from 14.32 to 67.95%. Large number interactions indicate the complexity of genetic architecture of resistance to stem rot disease. A QTL of physical map length 5.2 Mb identified on B04 comprising 170 different genes especially leucine reach repeats, zinc finger motifs and ethyleneresponsivefactors, etc., was identified. The identified genomic regions and candidate genes will further validate and facilitate marker development to deploy GAB for developing stem rot disease resistance groundnut varieties.

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. The genome sequence of segmental allotetraploid peanut suggests that diversity generated by genetic deletions and homeologous recombination helped to favor the domestication of Arachis hypogaea over its diploid relatives.