Multi-omics-driven advances in the understanding of triacylglycerol biosynthesis in oil seeds.

Vegetable oils are rich sources of polyunsaturated fatty acids and energy as well as valuable sources of human food, animal feed, and bioenergy. Triacylglycerols, which are comprised of three fatty acids attached to a glycerol backbone, are the main component of vegetable oils. Here, we review the development and application of multiple-level omics in major oilseeds and emphasize the progress in the analysis of the biological roles of key genes underlying seed oil content and quality in major oilseeds. Finally, we discuss future research directions in functional genomics research based on current omics and oil metabolic engineering strategies that aim to enhance seed oil content and quality, and specific fatty acids components according to either human health needs or industrial requirements.

Integrated physiological, transcriptomic and metabolomic analyses reveal the mechanism of peanut kernel weight reduction under waterlogging stress.

Waterlogging stress (WS) hinders kernel development and directly reduces peanut yield; however, the mechanism of kernel filling in response to WS remains unknown. The waterlogging-sensitive variety Huayu 39 was subjected to WS for 3 days at 7 days after the gynophores touched the ground (DAG). We found that WS affected kernel filling at 14, 21, and 28 DAG. WS decreased the average filling rate and kernel dry weight, while transcriptome sequencing and widely targeted metabolomic analysis revealed that WS inhibited the gene expression in starch and sucrose metabolism, which reduced sucrose input and transformation ability. Additionally, genes related to ethylene and melatonin synthesis and the accumulation of tryptophan and methionine were upregulated in response to WS. WS upregulated the expression of the gene encoding tryptophan decarboxylase (AhTDC), and overexpression of AhTDC in Arabidopsis significantly reduced the seed length, width, and weight. Therefore, WS reduced the kernel-filling rate, leading to a reduction in the 100-kernel weight. This survey informs the development of measures that alleviate the negative impact of WS on peanut yield and quality and provides a basis for exploring high-yield and high-quality cultivation, molecular-assisted breeding, and waterlogging prevention in peanut farming.

Identification of QTL for kernel weight and size and analysis of the pentatricopeptide repeat (PPR) gene family in cultivated peanut (Arachis hypogaea L.).

Peanut (Arachis hypogaea L.) is an important oilseed crop worldwide. Improving its yield is crucial for sustainable peanut production to meet increasing food and industrial requirements. Deciphering the genetic control underlying peanut kernel weight and size, which are essential components of peanut yield, would facilitate high-yield breeding. A high-density single nucleotide polymorphism (SNP)-based linkage map was constructed using a recombinant inbred lines (RIL) population derived from a cross between the variety Yuanza9102 and a germplasm accession wt09-0023. Kernel weight and size quantitative trait loci (QTLs) were co-localized to a 0.16 Mb interval on Arahy07 using inclusive composite interval mapping (ICIM). Analysis of SNP, and Insertion or Deletion (INDEL) markers in the QTL interval revealed a gene encoding a pentatricopeptide repeat (PPR) superfamily protein as a candidate closely linked with kernel weight and size in cultivated peanut. Examination of the PPR gene family indicated a high degree of collinearity of PPR genes between A. hypogaea and its diploid progenitors, Arachis duranensis and Arachis ipaensis. The candidate PPR gene, Arahy.JX1V6X, displayed a constitutive expression pattern in developing seeds. These findings lay a foundation for further fine mapping of QTLs related to kernel weight and size, as well as validation of candidate genes in cultivated peanut.

The determination of peanut (Arachis hypogaea L.) pod-sizes during the rapid-growth stage by phytohormones.

BACKGROUND: Pod size is an important yield target trait for peanut breeding. However, the molecular mechanism underlying the determination of peanut pod size still remains unclear. RESULTS: In this study, two peanut varieties with contrasting pod sizes were used for comparison of differences on the transcriptomic and endogenous hormonal levels. Developing peanut pods were sampled at 10, 15, 20, 25 and 30 days after pegging (DAP). Our results showed that the process of peanut pod-expansion could be divided into three stages: the gradual-growth stage, the rapid-growth stage and the slow-growth stage. Cytological analysis confirmed that the faster increase of cell-number during the rapid-growth stage was the main reason for the formation of larger pod size in Lps. Transcriptomic analyses showed that the expression of key genes related to the auxin, the cytokinin (CK) and the gibberellin (GA) were mostly up-regulated during the rapid-growth stage. Meanwhile, the cell division-related differentially expressed genes (DEGs) were mostly up-regulated at 10DAP which was consistent with the cytological-observation. Additionally, the absolute quantification of phytohormones were carried out by liquid-chromatography coupled with the tandem-mass-spectrometry (LC-MS/MS), and results supported the findings from comparative transcriptomic studies. CONCLUSIONS: It was speculated that the differential expression levels of TAA1 and ARF (auxin-related), IPT and B-ARR (CK-related), KAO, GA20ox and GA3ox (GA-related), and certain cell division-related genes (gene-LOC112747313 and gene-LOC112754661) were important participating factors of the determination-mechanism of peanut pod sizes. These results were informative for the elucidation of the underlying regulatory network in peanut pod-growth and would facilitate further identification of valuable target genes.

Transcriptome analysis provides insights into the stress response in cultivated peanut (Arachis hypogaea L.) subjected to drought-stress.

BACKGROUND: Peanut (Arachis hypogaea L.) is one of the valuable oilseed crops grown in drought-prone areas worldwide. Drought severely limits peanut production and productivity significantly. METHOD AND RESULTS: In order to decipher the drought tolerance mechanism in peanut under drought stress, RNA sequencing was performed in TAG - 24 (drought tolerant genotype) and JL-24 (drought susceptible genotype). Approximately 51 million raw reads were generated from four different libraries of two genotypes subjected to drought stress exerted by 20% PEG 6000 stress and control conditions, of which ~ 41 million (80.87%) filtered reads were mapped to the Arachis hypogaea L. reference genome. The transcriptome analysis detected 1,629 differentially expressed genes (DEGs), 186 genes encoding transcription factors (TFs) and 30,199 SSR among the identified DEGs. Among the differentially expressed TF encoding genes, the highest number of genes were WRKY followed by bZIP, C2H2, and MYB during drought stress. The comparative analysis between the two genotypes revealed that TAG-24 exhibits activation of certain key genes and transcriptional factors that are involved in essential biological processes. Specifically, TAG-24 showed activation of genes involved in the plant hormone signaling pathway such as PYL9, Auxin response receptor gene, and ABA. Additionally, genes related to water deprivation such as LEA protein and those involved in combating oxidative damage such as Glutathione reductase were also found to be activated in TAG-24. CONCLUSION: This genome-wide transcription map, therefore, provides a valuable tool for future transcript profiling under drought stress and enriches the genetic resources available for this important oilseed crop.

GWAS and bulked segregant analysis reveal the Loci controlling growth habit-related traits in cultivated Peanut (Arachis hypogaea L.).

BACKGROUND: Peanut (Arachis hypogaea L.) is a grain legume crop that originated from South America and is now grown around the world. Peanut growth habit affects the variety's adaptability, planting patterns, mechanized harvesting, disease resistance, and yield. The objective of this study was to map the quantitative trait locus (QTL) associated with peanut growth habit-related traits by combining the genome-wide association analysis (GWAS) and bulked segregant analysis sequencing (BSA-seq) methods. RESULTS: GWAS was performed with 17,223 single nucleotide polymorphisms (SNPs) in 103 accessions of the U.S. mini core collection genotyped using an Affymetrix version 2.0 SNP array. With a total of 12,342 high-quality polymorphic SNPs, the 90 suggestive and significant SNPs associated with lateral branch angle (LBA), main stem height (MSH), lateral branch height (LBL), extent radius (ER), and the index of plant type (IOPT) were identified. These SNPs were distributed among 15 chromosomes. A total of 597 associated candidate genes may have important roles in biological processes, hormone signaling, growth, and development. BSA-seq coupled with specific length amplified fragment sequencing (SLAF-seq) method was used to find the association with LBA, an important trait of the peanut growth habit. A 4.08 Mb genomic region on B05 was associated with LBA. Based on the linkage disequilibrium (LD) decay distance, we narrowed down and confirmed the region within the 160 kb region (144,193,467-144,513,467) on B05. Four candidate genes in this region were involved in plant growth. The expression levels of Araip.E64SW detected by qRT-PCR showed significant difference between 'Jihua 5' and 'M130'. CONCLUSIONS: In this study, the SNP (AX-147,251,085 and AX-144,353,467) associated with LBA by GWAS was overlapped with the results in BSA-seq through combined analysis of GWAS and BSA-seq. Based on LD decay distance, the genome range related to LBA on B05 was shortened to 144,193,467-144,513,467. Three candidate genes related to F-box family proteins (Araip.E64SW, Araip.YG1LK, and Araip.JJ6RA) and one candidate gene related to PPP family proteins (Araip.YU281) may be involved in plant growth and development in this genome region. The expression analysis revealed that Araip.E64SW was involved in peanut growth habits. These candidate genes will provide molecular targets in marker-assisted selection for peanut growth habits.

Genome-wide identification, evolutionary and expression analyses of LEA gene family in peanut (Arachis hypogaea L.).

BACKGROUND: Late embryogenesis abundant (LEA) proteins are a group of highly hydrophilic glycine-rich proteins, which accumulate in the late stage of seed maturation and are associated with many abiotic stresses. However, few peanut LEA genes had been reported, and the research on the number, location, structure, molecular phylogeny and expression of AhLEAs was very limited. RESULTS: In this study, 126 LEA genes were identified in the peanut genome through genome-wide analysis and were further divided into eight groups. Sequence analysis showed that most of the AhLEAs (85.7%) had no or only one intron. LEA genes were randomly distributed on 20 chromosomes. Compared with tandem duplication, segmental duplication played a more critical role in AhLEAs amplication, and 93 segmental duplication AhLEAs and 5 pairs of tandem duplication genes were identified. Synteny analysis showed that some AhLEAs genes come from a common ancestor, and genome rearrangement and translocation occurred among these genomes. Almost all promoters of LEAs contain ABRE, MYB recognition sites, MYC recognition sites, and ERE cis-acting elements, suggesting that the LEA genes were involved in stress response. Gene transcription analyses revealed that most of the LEAs were expressed in the late stages of peanut embryonic development. LEA3 (AH16G06810.1, AH06G03960.1), and Dehydrin (AH07G18700.1, AH17G19710.1) were highly expressed in roots, stems, leaves and flowers. Moreover, 100 AhLEAs were involved in response to drought, low-temperature, or Al stresses. Some LEAs that were regulated by different abiotic stresses were also regulated by hormones including ABA, brassinolide, ethylene and salicylic acid. Interestingly, AhLEAs that were up-regulated by ethylene and salicylic acid showed obvious subfamily preferences. Furthermore, three AhLEA genes, AhLEA1, AhLEA3-1, and AhLEA3-3, which were up-regulated by drought, low-temperature, or Al stresses was proved to enhance cold and Al tolerance in yeast, and AhLEA3-1 enhanced the drought tolerance in yeast. CONCLUSIONS: AhLEAs are involved in abiotic stress response, and segmental duplication plays an important role in the evolution and amplification of AhLEAs. The genome-wide identification, classification, evolutionary and transcription analyses of the AhLEA gene family provide a foundation for further exploring the LEA genes' function in response to abiotic stress in peanuts.

Transcriptome Analysis and Gene Expression Profiling of the Peanut Small Seed Mutant Identified Genes Involved in Seed Size Control.

Seed size is a key factor affecting crop yield and a major agronomic trait concerned in peanut (Arachis hypogaea L.) breeding. However, little is known about the regulation mechanism of peanut seed size. In the present study, a peanut small seed mutant1 (ssm1) was identified through irradiating peanut cultivar Luhua11 (LH11) using 60Coγ ray. Since the globular embryo stage, the embryo size of ssm1 was significantly smaller than that of LH11. The dry seed weight of ssm1 was only 39.69% of the wild type LH14. The seeds were wrinkled with darker seed coat. The oil content of ssm1 seeds were also decreased significantly. Seeds of ssm1 and LH11 were sampled 10, 20, and 40 days after pegging (DAP) and were used for RNA-seq. The results revealed that genes involved in plant hormones and several transcription factors related to seed development were differentially expressed at all three stages, especially at DAP10 and DAP20. Genes of fatty acid biosynthesis and late embryogenesis abundant protein were significantly decreased to compare with LH11. Interestingly, the gene profiling data suggested that PKp2 and/or LEC1 could be the key candidate genes leading to the small seed phenotype of the mutant. Our results provide valuable clues for further understanding the mechanisms underlying seed size control in peanut.

Comparative Multi-Omics Analysis Reveals Lignin Accumulation Affects Peanut Pod Size.

Pod size is one of the important factors affecting peanut yield. However, the metabolites relating to pod size and their biosynthesis regulatory mechanisms are still unclear. In the present study, two peanut varieties (Tif and Lps) with contrasting pod sizes were used for a comparative metabolome and transcriptome analysis. Developing peanut pods were sampled at 10, 20 and 30 days after pegging (DAP). A total of 720 metabolites were detected, most of which were lipids (20.3%), followed by phenolic acids (17.8%). There were 43, 64 and 99 metabolites identified as differentially accumulated metabolites (DAMs) at 10, 20 and 30 DAP, respectively, and flavonoids were the major DAMs between Tif and Lps at all three growth stages. Multi-omics analysis revealed that DAMs and DEGs (differentially expressed genes) were significantly enriched in the phenylpropanoid biosynthesis (ko00940) pathway, the main pathway of lignin biosynthesis, in each comparison group. The comparisons of the metabolites in the phenylpropanoid biosynthesis pathway accumulating in Tif and Lps at different growth stages revealed that the accumulation of p-coumaryl alcohol (H-monolignol) in Tif was significantly greater than that in Lps at 30 DAP. The differential expression of gene-LOC112771695, which is highly correlated with p-coumaryl alcohol and involved in the biosynthesis of monolignols, between Tif and Lps might explain the differential accumulation of p-coumaryl alcohol. The content of H-lignin in genetically diverse peanut varieties demonstrated that H-lignin content affected peanut pod size. Our findings would provide insights into the metabolic factors influencing peanut pod size and guidance for the genetic improvement of the peanut.

Optimization of Protoplast Isolation and Transformation for a Pilot Study of Genome Editing in Peanut by Targeting the Allergen Gene Ara h 2.

The cultivated peanut (Arachis hypogaea L.) is a legume consumed worldwide in the form of oil, nuts, peanut butter, and candy. Improving peanut production and nutrition will require new technologies to enable novel trait development. Clustered regularly interspaced short palindromic repeats and CRISPR-associated protein 9 (CRISPR-Cas9) is a powerful and versatile genome-editing tool for introducing genetic changes for studying gene expression and improving crops, including peanuts. An efficient in vivo transient CRISPR-Cas9- editing system using protoplasts as a testbed could be a versatile platform to optimize this technology. In this study, multiplex CRISPR-Cas9 genome editing was performed in peanut protoplasts to disrupt a major allergen gene with the help of an endogenous tRNA-processing system. In this process, we successfully optimized protoplast isolation and transformation with green fluorescent protein (GFP) plasmid, designed two sgRNAs for an allergen gene, Ara h 2, and tested their efficiency by in vitro digestion with Cas9. Finally, through deep-sequencing analysis, several edits were identified in our target gene after PEG-mediated transformation in protoplasts with a Cas9 and sgRNA-containing vector. These findings demonstrated that a polyethylene glycol (PEG)-mediated protoplast transformation system can serve as a rapid and effective tool for transient expression assays and sgRNA validation in peanut.

First comprehensive proteomics analysis of lysine crotonylation in leaves of peanut (Arachis hypogaea L.).

Lysine crotonylation is an important post-translational modification process. Most research in this area has been carried out on mammals and yeast, but there has been little research on it in plants. In the current study, large-scale lysine crotonylome analysis was performed by a combination of affinity enrichment and high-resolution LC-MS/MS analysis. Altogether, 6051 lysine crotonylation sites were identified in 2508 protein groups. Bioinformatics analysis showed that lysine-crotonylated proteins were involved in many biological processes, such as carbon fixation in photosynthetic organisms, biosynthesis of amino acids, ribosomes structure and function. In particular, subcellular localization analysis showed that 43% of the crotonylated proteins were located in the chloroplast. Twenty-nine crotonylation proteins were associated with photosynthesis and functional enrichment that these proteins were associated with the reaction center, photosynthetic electron transport, and ATP synthesis. Based on these results, further studies to expand on the lysine crotonylome analysis were suggested.

Comparative transcriptome analysis of genes involved in the drought stress response of two peanut (Arachis hypogaea L.) varieties.

BACKGROUND: The peanut is one of the most important oil crops worldwide. Qualities and yields of peanut can be dramatically diminished by abiotic stresses particularly by drought. Therefore, it would be beneficial to gain a comprehensive understanding on peanut drought-responsive transcriptional regulatory activities, and hopefully to extract critical drought-tolerance-related molecular mechanism from it. RESULTS: In this study, two peanut Arachis hypogaea L. varieties, NH5 (tolerant) and FH18 (sensitive), which show significantly differential drought tolerance, were screened from 23 main commercial peanut cultivars and used for physiological characterization and transcriptomic analysis. NH5 leaves showed higher water and GSH contents, faster stomatal closure, and lower relative conductivity (REC) than FH18. Under the time-course of drought-treatments 0 h (CK), 4 h (DT1), 8 h (DT2) and 24 h (DT3), the number of down-regulated differential expressed genes (DEGs) increased with the progression of treatments indicating repressive impacts on transcriptomes by drought in both peanut varieties. CONCLUSIONS: Nevertheless, NH5 maintained more stable transcriptomic dynamics than FH18. Furthermore, annotations of identified DEGs implicate signal transduction, the elimination of reactive oxygen species, and the maintenance of cell osmotic potential which are key drought-tolerance-related pathways. Finally, evidences from the examination of ABA and SA components suggested that the fast stomatal closure in NH5 was likely mediated through SA rather than ABA signaling. In all, these results have provided us a comprehensive overview of peanut drought-responsive transcriptomic changes, which could serve as solid foundation for further identification of the molecular drought-tolerance mechanism in peanut and other oil crops.

Comprehensive effects of salt stress and peanut cultivars on the rhizosphere bacterial community diversity of peanut.

Plant rhizosphere bacterial communities are central to plant growth and stress tolerance, which differ across cultivars and external environments. The goal of this study was to assess the comprehensive effects of salt stress and peanut cultivars on rhizosphere bacterial community diversity. In this study, we investigated the effects of salt stress on peanut morphology and pod yield and the associated rhizosphere bacterial diversity using statistical analysis and 16S rRNA gene sequencing, respectively. Statistical analysis exhibited that salt stress indeed affected peanut growth and pod yield, and various peanut cultivars showed divergences. Taxonomic analysis showed that the bacterial community predominantly consisted of phyla Actinobacteria, Proteobacteria, Chloroflexi, Acidobacteria, and Cyanobacteria in peanut rhizosphere soils. Among these bacteria, numbers of beneficial bacteria Cyanobacteria and Proteobacteria increased, especially in the salt-resistant cultivars, while that of Acidobacteria decreased after salt treatment. Nitrogen-fixing bacterium Rhizobium closely related to peanut nodulation was significantly improved in rhizosphere soils of salt-resistant cultivars after salt treatment. Metabolic function prediction showed that the percentages of reads categorized to signaling transduction and inorganic ion transport and metabolism were higher in the salt-treated soils, which may be conducive to peanut survival and salt tolerance to some extent. The study is, therefore, crucially important to develop the foundation for improving the salt tolerance of various peanut cultivars via modifying the soil bacterial community.

Induction of pre-chorismate, jasmonate and salicylate pathways by Burkholderia sp. RR18 in peanut seedlings.

AIMS: To characterize the mechanisms by which bacteria in the peanut rhizosphere promote plant growth and suppress Aspergillus niger, the fungus that causes collar rot of peanut. METHODS AND RESULTS: In all, 131 isolates cultured from the peanut rhizosphere were assayed for growth promotion in a seedling germination assay. The most effective isolate, RR18, was identified as Burkholderia sp. by 16S sequencing analysis. RR18 reduced collar rot disease incidence and increased the germination rate and biomass of peanut seeds, and had broad-spectrum antifungal activity. Quantitative analyses showed that RR18 induced long-lasting accumulation of jasmonic acid, salicylic acid and phenols, and triggered the activity of six defence enzymes related to these changes. Comparative proteomic analysis of treated and untreated seedlings revealed a clear induction of four abundant proteins, including a member of the pre-chorismate pathway, a regulator of clathrin-coated vesicles, a transcription factor and a hypothetical protein. CONCLUSION: Burkholderia sp. RR18 promotes peanut growth and disease resistance, and stably induces two distinct defence pathways associated with systemic resistance. SIGNIFICANCE AND IMPACT OF THE STUDY: This study demonstrates that a strain of the Burkholderia cepacia complex can elicit both salicylic- and jasmonic-acid-mediated defences, in addition to having numerous other beneficial properties.

Transcriptome profiling provides insights into molecular mechanism in Peanut semi-dwarf mutant.

BACKGROUND: Plant height, mainly decided by main stem height, is the major agronomic trait and closely correlated to crop yield. A number of studies had been conducted on model plants and crops to understand the molecular and genetic basis of plant height. However, little is known on the molecular mechanisms of peanut main stem height. RESULTS: In this study, a semi-dwarf peanut mutant was identified from 60Co γ-ray induced mutant population and designated as semi-dwarf mutant 2 (sdm2). The height of sdm2 was only 59.3% of its wild line Fenghua 1 (FH1) at the mature stage. The sdm2 has less internode number and short internode length to compare with FH1. Gene expression profiles of stem and leaf from both sdm2 and FH1 were analyzed using high throughput RNA sequencing. The differentially expressed genes (DEGs) were involved in hormone biosynthesis and signaling pathways, cell wall synthetic and metabolic pathways. BR, GA and IAA biosynthesis and signal transduction pathways were significantly enriched. The expression of several genes in BR biosynthesis and signaling were found to be significantly down-regulated in sdm2 as compared to FH1. Many transcription factors encoding genes were identified as DEGs. CONCLUSIONS: A large number of genes were found differentially expressed between sdm2 and FH1. These results provide useful information for uncovering the molecular mechanism regulating peanut stem height. It could facilitate identification of causal genes for breeding peanut varieties with semi-dwarf phenotype.

Transcriptome and metabolome reveal redirection of flavonoids in a white testa peanut mutant.

BACKGROUND: Coat color determines both appearance and nutrient quality of peanut. White seed coat in peanut can enhance the processing efficiency and quality of peanut oil. An integrative analysis of transcriptomes, metabolomes and histocytology was performed on wsc mutant and its wild type to investigate the regulatory mechanisms underlying color pigmentation. RESULT: Metabolomes revealed flavonoids were redirected in wsc, while multi-omics analyses of wsc mutant seeds and testae uncovered WSC influenced the flavonoids biosynthesis in testa as well as suberin formation, glycolysis, the TCA cycle and amino acid metabolism. The mutation also enhanced plant hormones synthesis and signaling. Further, co-expression analysis showed that FLS genes co-expressed with MBW complex member genes. Combining tissue expression patterns, genetic analyses, and the annotation of common DEGs for these three stages revealed that three testa specific expressed candidate genes, Araip.M7RY3, Aradu.R8PMF and Araip.MHR6K were likely responsible for the white testa phenotype. WSC might be regulated expression competition between FLS and DFR by controlling hormone synthesis and signaling as well as the MBW complex. CONCLUSIONS: The results of this study therefore provide both candidate genes and novel approaches that can be applied to improve peanut with desirable seed coat color and flavonoid quality.

Discovery, identification, and functional characterization of long noncoding RNAs in Arachis hypogaea L.

BACKGROUND: Long noncoding RNAs (lncRNAs), which are typically > 200 nt in length, are involved in numerous biological processes. Studies on lncRNAs in the cultivated peanut (Arachis hypogaea L.) largely remain unknown. RESULTS: A genome-wide scan of the peanut (Arachis hypogaea L.) transcriptome identified 1442 lncRNAs, which were encoded by loci distributed over every chromosome. Long intergenic noncoding RNAs accounted for 85.58% of these lncRNAs. Additionally, 189 lncRNAs were differentially abundant in the root, leaf, or seed. Generally, lncRNAs showed lower expression levels, tighter tissue-specific expression, and less splicing than mRNAs. Approximately 44.17% of the lncRNAs with an exon/intron structure were alternatively spliced; this rate was slightly lower than the splicing rate of mRNA. Transcription at the start site event was the alternative splicing (AS) event with the highest frequency (28.05%) in peanut lncRNAs, whereas the occurrence rate (30.19%) of intron retention event was the highest in mRNAs. AS changed the target gene profiles of lncRNAs and increased the diversity and flexibility of lncRNAs, which may be important for lncRNAs to execute their functions. Additionally, a substantial number of the peanut AS isoforms generated from protein-encoding genes appeared to be noncoding because they were truncated transcripts; such isoforms can be legitimately regarded as a class of lncRNAs. The predicted target genes of the lncRNAs were involved in a wide range of biological processes. Furthermore, expression pattern of several selected lncRNAs and their target genes were examined under salt stress, results showed that all of them could respond to salt stress in different manners. CONCLUSIONS: This study provided a resource of candidate lncRNAs and expression patterns across tissues, and whether these lncRNAs are functional will be further investigated in our subsequent experiments.

Ectopic expression of MYB repressor GmMYB3a improves drought tolerance and productivity of transgenic peanuts (Arachis hypogaea L.) under conditions of water deficit.

Peanut is widely grown and provides protein and edible oil for millions of people. Peanut growth and productivity are frequently negatively affected by abiotic and biotic environmental factors. However, the research on improving peanut germplasm resources by genetic transformation is very limited. Here, the novel R2R3-MYB repressor GmMYB3a was introduced into peanut plants by Agrobacterium-mediated transformation for the first time for thorough evaluation of the function of GmMYB3a in drought stress plant responses. We generated GmMYB3a-transgenic peanut plants. The GmMYB3a-overexpressing lines showed significantly improved physiological responses and no yield loss non-transgenic plants, in terms of survival rates. Thus, the GmMYB3a-overexpressing plants showed better photosynthetic performance, higher relative water content, and greater water use efficiency, demonstrating their adaptive capacity to water deficit. We conclude that overexpression of GmMYB3a can improve drought tolerance and productivity in peanut.

Bradyrhizobium sp. enhance ureide metabolism increasing peanuts yield.

This study aimed to evaluate the effects of seed inoculation with Bradyrhizobium sp. and co-inoculation with Azospirillum brasilense. The seed treatments were as follows: control (without inoculation); A. brasilense (2 mL per kg-1 of seed); A. brasilense (4 mL per kg-1 of seed); Bradyrhizobium sp. (2 mL per kg-1 of seed); Bradyrhizobium sp. (4 mL per kg-1 of seed); A. brasilense + Bradyrhizobium sp. (2 mL of each strain per kg-1 of seed); and A. brasilense + Bradyrhizobium sp. (4 mL of each strain per kg-1 of seed). Peanut plants from seeds inoculated with Bradyrhizobium sp. and A. brasilense exhibited highest leaf concentration of photosynthetic pigments, carotenoids, nitrate, ammonia and amino acids. The inoculation of seeds with Bradyrhizobium sp. resulted in plants with increased concentrations of total soluble sugars, and ureides compared to the untreated plants. In contrast, seeds treated with A. brasilense alone resulted in plants exhibiting highest concentration of amino acids, which represent the highest concentration of nitrogen compounds in peanut plants. Seed inoculation with Bradyrhizobium sp. at a rate of 2 mL kg-1 was identified as the best treatment to promote increased biological nitrogen fixation and generate higher peanut yields.

Influence of salt stress on the rhizosphere soil bacterial community structure and growth performance of groundnut (Arachis hypogaea L.).

Soil salinity is regarded as severe environmental stress that can change the composition of rhizosphere soil bacterial community and import a plethora of harms to crop plants. However, relatively little is known about the relationship between salt stress and root microbial communities in groundnuts. The goal of this study was to assess the effect of salt stress on groundnut growth performance and rhizosphere microbial community structure. Statistical analysis exhibited that salt stress indeed affected groundnut growth and pod yield. Further taxonomic analysis showed that the bacterial community predominantly consisted of phyla Proteobacteria, Actinobacteria, Saccharibacteria, Chloroflexi, Acidobacteria, and Cyanobacteria. Among these bacteria, numbers of Cyanobacteria and Acidobacteria mainly increased, while that of Actinobacteria and Chloroflexi decreased after salt treatment via taxonomic and qPCR analysis. Moreover, Sphingomonas and Microcoleus as the predominant genera in salt-treated rhizosphere soils might enhance salt tolerance as plant growth-promoting rhizobacteria. Metagenomic profiling showed that series of sequences related to signaling transduction, posttranslational modification, and chaperones were enriched in the salt-treated soils, which may have implications for plant survival and salt tolerance. These data will help us better understand the symbiotic relationship between the dominant microbial community and groundnuts and form the foundation for further improvement of salt tolerance of groundnuts via modification of soil microbial community.