Background: Basic helix-loop-helix (bHLH) transcription factors (TFs) are one of the largest gene families in plants. They regulate gene expression through interactions with specific motifs in target genes. bHLH TFs are not only universally involved in plant growth but also play an important role in plant responses to abiotic stress. However, most members of this family have not been functionally characterized. Results: Here, we characterized the function of a bHLH TF in the peanut, AhHLH112, in response to drought stress. AhHLH112 is localized in the nucleus and it was induced by drought stress. The overexpression of this gene improves the drought tolerance of transgenic plants both in seedling and adult stages. Compared to wild-type plants, the transgenic plants accumulated less reactive oxygen species (ROS), accompanied by increased activity and transcript levels of antioxidant enzymes (superoxide dismutase, peroxidase and catalase). In addition, the WT plants demonstrated higher MDA concentration levels and higher water loss rate than the transgenic plants under drought treatment. The Yeast one-hybrid result also demonstrates that AhbHLH112 directly and specifically binds to and activates the promoter of the peroxidase (POD) gene. Besides, overexpression of AhHLH112 improved ABA level under drought condition, and elevated the expression of genes associated with ABA biosynthesis and ABA responding, including AtNCED3 and AtRD29A. Conclusions: Drawing on the results of our experiments, we propose that, by improving ROS-scavenging ability, at least in part through the regulation of POD -mediated H₂O₂ homeostasis, and possibly participates in ABA-dependent stress-responding pathway, AhbHLH112 acts as a positive factor in drought stress tolerance.

Peanut (Arachis hypogaea L.) is one of the most important oil crops worldwide, and its yet increasing market demand may be met by genetic improvement of yield related traits, which may be facilitated by a good understanding of the underlying genetic base of these traits. Here, we have carried out a genome-wide association study (GWAS) with the aim to identify genomic regions and the candidate genes within these regions that may be involved in determining the phenotypic variation at seven yield-related traits in peanut. For the GWAS analyses, 195 peanut accessions were phenotyped and/or genotyped; the latter was done using a genotyping-by-sequencing approach, which produced a total of 13,435 high-quality single nucleotide polymorphisms (SNPs). Analyses of these SNPs show that the analyzed peanut accessions can be approximately grouped into two big groups that, to some extent, agree with the botanical classification of peanut at the subspecies level. By taking this genetic structure as well as the relationships between the analyzed accessions into consideration, our GWAS analyses have identified 93 non-overlapping peak SNPs that are significantly associated with four of the studied traits. Gene annotation of the genome regions surrounding these peak SNPs have found a total of 311 unique candidate genes. Among the 93 yield-related-trait-associated SNP peaks, 12 are found to be co-localized with the quantitative trait loci (QTLs) that were identified by earlier related QTL mapping studies, and these 12 SNP peaks are only related to three traits and are almost all located on chromosomes Arahy.05 and Arahy.16. Gene annotation of these 12 co-localized SNP peaks have found 36 candidates genes, and a close examination of these candidate genes found one very interesting gene (arahy.RI9HIF), the rice homolog of which produces a protein that has been shown to improve rice yield when over-expressed. Further tests of the arahy.RI9HIF gene, as well as other candidate genes especially those within the more confident co-localized genomic regions, may hold the potential for significantly improving peanut yield.

12-oxo-phytodienoic acid reductases (OPRs) have been substantiated as pivotal in plant growth and response to biotic and abiotic stresses. However, the functional characterization of OPR genes in the peanut genome remains limited. In this study, we identified a total of 20 OPR genes in a tetraploid cultivar and two diploid peanut species, categorizing them into two subfamilies, OPRI and OPRII. The gene structure and conserved protein motifs within each subfamily were elucidated. Additionally, our findings indicate an uneven chromosomal distribution of peanut OPR genes. Gene duplication events were identified as pivotal in the expansion of the OPR gene family. An analysis of cis-acting elements within OPR gene promoters revealed the presence of numerous phytohormone- and stress-related cis-elements. Furthermore, peanut OPR genes exhibited tissue-specific and stress-inducible expression patterns, underscoring their crucial role in peanut growth and stress response. Additionally, plants overexpressing AhOPR6 exhibited significantly enhanced resistance to salt stress, and the AhOPR6-OE lines demonstrated a higher ability to scavenge reactive oxygen species (ROS). Collectively, these findings offer deeper insights into the roles of peanut OPR genes in stress responses, suggesting that AhOPR6 could serve as a potential candidate gene for improving peanut salt tolerance through genetic transformation.

Background: The cultivated peanut (Arachis hypogaea) is one of the most important oilseed crops worldwide, however, its improvement is restricted by its narrow genetic base. The highly variable wild peanut species, especially within Sect.Arachis, may serve as a rich genetic source of favorable alleles to peanut improvement; Sect.Arachisis the biggest taxonomic section within genusArachisand its members also include the cultivated peanut. In order to make good use of these wild resources, the genetic bases and the relationships of theArachisspecies need first to be better understood.Results: Here, in this study, we have sequenced and/or assembled twelveArachiscomplete chloroplast (cp) genomes (eleven from Sect.Arachis). These cp genome sequences enriched the publishedArachiscp genome data. From the twelve acquired cp genomes, substantial genetic variation (1368 SNDs, 311 indels) has been identified, which, together with 69 SSR loci that have been identified from the same data set, will provide powerful tools for future explorations. Phylogenetic analyses in our study have grouped the Sect.Arachisspecies into two major lineages (I & II), this result together with reports from many earlier studies show that lineage II is dominated by AA genome species that are mostly perennial, while lineage I includes species that have more diverse genome types and are mostly annual/biennial. Moreover, the cultivated peanuts andA.monticolathat are the only tetraploid (AABB) species withinArachisare nested within the AA genome species-dominated lineage, this result together with the maternal inheritance of chloroplast indicate a maternal origin of the two tetraploid species from an AA genome species.Conclusion: In summary, we have acquired sequences of twelve completeArachiscp genomes, which have not only helped us better understand how the cultivated peanut and its close wild relatives are related, but also provided us with rich genetic resources that may hold great potentials for future peanut breeding.

Long non-coding RNAs (lncRNAs) are involved in various regulatory processes although they do not encode protein. Presently, there is little information regarding the identification of lncRNAs in peanut (Arachis hypogaea Linn.). In this study, 50,873 lncRNAs of peanut were identified from large-scale published RNA sequencing data that belonged to 124 samples involving 15 different tissues. The average lengths of lncRNA and mRNA were 4335 bp and 954 bp, respectively. Compared to the mRNAs, the lncRNAs were shorter, with fewer exons and lower expression levels. The 4713 co-expression lncRNAs (expressed in all samples) were used to construct co-expression networks by using the weighted correlation network analysis (WGCNA). LncRNAs correlating with the growth and development of different peanut tissues were obtained, and target genes for 386 hub lncRNAs of all lncRNAs co-expressions were predicted. Taken together, these findings can provide a comprehensive identification of lncRNAs in peanut.