Peanut Gene Research Articles

Genome-Wide Investigation of Apyrase (APY) Genes in Peanut (Arachis hypogaea L.) and Functional Characterization of a Pod-Abundant Expression Promoter AhAPY2-1p

Peanut (Arachis hypogaea L.) is an important food and feed crop worldwide and is affected by various biotic and abiotic stresses. The cellular ATP levels decrease significantly during stress as ATP molecules move to extracellular spaces, resulting in increased ROS production and cell apoptosis. Apyrases (APYs) are the nucleoside phosphatase (NPTs) superfamily members and play an important role in regulating cellular ATP levels under stress. We identified 17 APY homologs in A. hypogaea (AhAPYs), and their phylogenetic relationships, conserved motifs, putative miRNAs targeting different AhAPYs, cis-regulatory elements, etc., were studied in detail. The transcriptome expression data were used to observe the expression patterns in different tissues and under stress conditions. We found that the AhAPY2-1 gene showed abundant expression in the pericarp. As the pericarp is a key defense organ against environmental stress and promoters are the key elements regulating gene expression, we functionally characterized the AhAPY2-1 promoter for its possible use in future breeding programs. The functional characterization of AhAPY2-1P in transgenic Arabidopsis plants showed that it effectively regulated GUS gene expression in the pericarp. GUS expression was also detected in flowers of transgenic Arabidopsis plants. Overall, these results strongly suggest that APYs are an important future research subject for peanut and other crops, and AhPAY2-1P can be used to drive the resistance-related genes in a pericarp-specific manner to enhance the defensive abilities of the pericarp.

Genome-wide identification of papain-like cysteine protease family genes in cultivated peanut (Arachis hypogaea L.) and functional characterization of AhRD21B in response to chilling stress

Papain-like cysteine proteases (PLCPs) play essential roles in plant growth, senescence, and stress responses. However, researches on the PLCP genes are limited in cultivated peanut (Arachis hypogaea L.). Here, we identified and analyzed AhPLCP genes in cultivated peanut using bioinformatic approaches and verified the involvement of AhRD21B in response to chilling tolerance using an experimental test. We identified 52 AhPLCP genes in peanut genome and categorized them into eight subfamilies. Six tandem duplicated genes were identified in cultivated peanut. The promoters of AhPLCP genes contained many stress responsive elements. AhPLCP genes were generally expressed constitutively, and many AhPLCP genes were cold-responsive. Among these genes, heterologous expression of AhRD21B significantly increased the tolerance of transgenic Arabidopsis to cold compared with the wild-type plants. In addation, AhRD21B can regulate cold-related genes that participate in enhancing chilling tolerance in transgenic Arabidopsis. These findings provide valuable insights into the functions of AhPLCP genes in plant stress tolerance.

Genome-wide analysis of R2R3-MYB genes in cultivated peanut (Arachis hypogaea L.): Gene duplications, functional conservation, and diversification.

The cultivated Peanut (Arachis hypogaea L.), an important oilseed and edible legume, are widely grown worldwide. The R2R3-MYB transcription factor, one of the largest gene families in plants, is involved in various plant developmental processes and responds to multiple stresses. In this study we identified 196 typical R2R3-MYB genes in the genome of cultivated peanut. Comparative phylogenetic analysis with Arabidopsis divided them into 48 subgroups. The motif composition and gene structure independently supported the subgroup delineation. Collinearity analysis indicated polyploidization, tandem, and segmental duplication were the main driver of the R2R3-MYB gene amplification in peanut. Homologous gene pairs between the two subgroups showed tissue specific biased expression. In addition, a total of 90 R2R3-MYB genes showed significant differential expression levels in response to waterlogging stress. Furthermore, we identified an SNP located in the third exon region of AdMYB03-18 (AhMYB033) by association analysis, and the three haplotypes of the SNP were significantly correlated with total branch number (TBN), pod length (PL) and root-shoot ratio (RS ratio), respectively, revealing the potential function of AdMYB03-18 (AhMYB033) in improving peanut yield. Together, these studies provide evidence for functional diversity in the R2R3-MYB genes and will contribute to understanding the function of R2R3-MYB genes in peanut.

Genome-wide characterization of phospholipase D family genes in allotetraploid peanut and its diploid progenitors revealed their crucial roles in growth and abiotic stress responses.

Abiotic stresses such as cold, drought and salinity are the key environmental factors that limit the yield and quality of oil crop peanut. Phospholipase Ds (PLDs) are crucial hydrolyzing enzymes involved in lipid mediated signaling and have valuable functions in plant growth, development and stress tolerance. Here, 22, 22 and 46 PLD genes were identified in Arachis duranensis, Arachis ipaensis and Arachis hypogaea, respectively, and divided into α, β, γ, δ, ε, ζ and φ isoforms. Phylogenetic relationships, structural domains and molecular evolution proved the conservation of PLDs between allotetraploid peanut and its diploid progenitors. Almost each A. hypogaea PLD except for AhPLDα6B had a corresponding homolog in A. duranensis and A. ipaensis genomes. The expansion of Arachis PLD gene families were mainly attributed to segmental and tandem duplications under strong purifying selection. Functionally, the most proteins interacting with AhPLDs were crucial components of lipid metabolic pathways, in which ahy-miR3510, ahy-miR3513-3p and ahy-miR3516 might be hub regulators. Furthermore, plenty of cis-regulatory elements involved in plant growth and development, hormones and stress responses were identified. The tissue-specific transcription profiling revealed the broad and unique expression patterns of AhPLDs in various developmental stages. The qRT-PCR analysis indicated that most AhPLDs could be induced by specific or multiple abiotic stresses. Especially, AhPLDα3A, AhPLDα5A, AhPLDβ1A, AhPLDβ2A and AhPLDδ4A were highly up-regulated under all three abiotic stresses, whereas AhPLDα9A was neither expressed in 22 peanut tissues nor induced by any abiotic stresses. This genome-wide study provides a systematic analysis of the Arachis PLD gene families and valuable information for further functional study of candidate AhPLDs in peanut growth and abiotic stress responses.

Genome-wide identification, evolutionary and expression analysis of the cyclin-dependent kinase gene family in peanut

BackgroundCyclin-dependent kinases (CDKs) are a predominant group of serine/threonine protein kinases that have multi-faceted functions in eukaryotes. The plant CDK members have well-known roles in cell cycle progression, transcriptional regulation, DNA repair, abiotic stress and defense responses, making them promising targets for developing stress adaptable high-yielding crops. There is relatively sparse information available on the CDK family genes of cultivated oilseed crop peanut and its diploid progenitors.ResultsWe have identified 52 putative cyclin-dependent kinases (CDKs) and CDK-like (CDKLs) genes in Arachis hypogaea (cultivated peanut) and total 26 genes in each diploid parent of cultivated peanut (Arachis duranensis and Arachis ipaensis). Both CDK and CDKL genes were classified into eight groups based on their cyclin binding motifs and their phylogenetic relationship with Arabidopsis counterparts. Genes in the same subgroup displayed similar exon–intron structure and conserved motifs. Further, gene duplication analysis suggested that segmental duplication events played major roles in the expansion and evolution of CDK and CDKL genes in cultivated peanuts. Identification of diverse cis-acting response elements in CDK and CDKL genes promoter indicated their potential fundamental roles in multiple biological processes. Various gene expression patterns of CDKs and CDKLs in different peanut tissues suggested their involvement during growth and development. In addition, qRT-PCR analysis demonstrated that most representing CDK and CDKL gene family members were significantly down-regulated under ABA, PEG and mannitol treatments.ConclusionsGenome-wide analysis offers a comprehensive understanding of the classification, evolution, gene structure, and gene expression profiles of CDK and CDKL genes in cultivated peanut and their diploid progenitors. Additionally, it also provides cell cycle regulatory gene resources for further functional characterization to enhance growth, development and abiotic stress tolerance.

Comprehensive Analysis of GASA Family Members in the Peanut Genome: Identification, Characterization, and Their Expressions in Response to Pod Development

The gibberellic acid-stimulated Arabidopsis (GASA) gene family is essential for plant growth and development, hormone level control, and phytohormone signal transmission. Different plants have been shown to contain numerous GASA homologs. However, there is no knowledge about these proteins in peanuts. In the current study, we performed a thorough bioinformatics and expression analysis and found 20, 22, and 40 GASA genes by genome-wide analyses of A. hypogaea L., A. duranensis, and A. ipaensis, respectively. We analyzed and predicted the physical properties of these genes. Based on the results of our phylogenetic analysis, the evolutionary tree constructed from the 40 AhGASA proteins was divided into seven categories, forming a total of 14 gene pairs. According to our observations, tandem duplication is a significant factor in the expansion of the GASA gene family. AhGASA was unevenly distributed on 20 chromosomes, and 17 tandem duplicated genes were identified. A co-lineage analysis with the A/B subgenome identified 69 linear/parallel homologous gene pairs. A cis-element analysis revealed that the AhGASA protein is crucial for hormone responsiveness. In materials with different size traits at various stages of peanut pod development, transcriptomics and RT-qPCR analyses revealed that AhGASA genes are expressed at various levels and are tissue-specific. This finding suggests that some AhGASA genes may be involved in controlling peanut pod size. This study suggests that GASA genes are crucial for controlling the development of peanut pods and provides the first systematic identification and analysis of GASA genes in peanut. These findings will help future research into the function of the GASA gene in the cultivated peanut.

Genomic analysis of sugar transporter genes in peanut (Arachis hypogaea): Characteristic, evolution and expression profiles during development and stress

Peanut (Arachis hypogaea L.) is an economically significant crop with aerial cleistogamous flowers and subterranean geocarpic fruit (pods). The formation of peanut pod requires movement of the embryo from air to ground and then development in the soil, which is a complex biological process involving transport and accumulation of sugars. Sugar transport proteins (STP) mediate the transport of monosaccharides in various physiological processes, including fertilization, ovary formation, and seed development. In this study, a total of 36 AhSTP genes (AhSTP1–36) containing the conserved sugar_tr motif were identified in the A. hypogaea genome. Phylogenetic analysis revealed that AhSTP genes were classified into four clades, and the arrangement of motifs in AhSTP proteins was similar within clades. Synteny analysis revealed that segmental duplication events have played an important role in the expansion of STP genes in peanut, and chromosome rearrangements might have facilitated the exchange of STP genes between the A and B sub-genomes. Transcriptome analyses revealed that the expression patterns of AhSTP genes varied among tissues. Hormone and abiotic stress treatments could up-regulate or down-regulate the expression of AhSTP genes, and low temperature had a major effect on the expression of most AhSTP genes. Four AhSTP genes (AhSTP3, AhSTP9, AhSTP19, and AhSTP28) were specifically expressed in the pod, indicating that these genes might be involved in pod formation and development in peanut. The unique expression of these four genes during pod construction and development was confirmed in two different type cultivars using quantitative real-time PCR analysis. Our findings provide new insights into the STP gene family in peanut and will aid future functional studies of AhSTP genes.

Identification, expression, and association analysis of calcineurin B-like protein-interacting protein kinase genes in peanut.

Plants usually respond to the external environment by initiating a series of signal transduction processes mediated by protein kinases, especially calcineurin B-like protein–interacting protein kinases (CIPKs). In this study, 54 CIPKs were identified in the peanut genome, of which 26 were from cultivated species (named AhCIPKs) and 28 from two diploid progenitors (Arachis duranensis—AdCIPKs and Arachis ipaensis—AiCIPKs). Evolution analysis revealed that the 54 CIPKs were composed of two different evolutionary branches. The CIPK members were unevenly distributed at different chromosomes. Synteny analysis strongly indicated that whole-genome duplication (allopolyploidization) contributed to the expansion of CIPK. Comparative genomics analysis showed that there was only one common collinear CIPK pairs among peanut, Arabidopsis, rice, grape, and soybean. The prediction results of cis-acting elements showed that AhCIPKs, AdCIPKs, and AiCIPKs contained different proportions of transcription factor binding motifs involved in regulating plant growth, abiotic stress, plant hormones, and light response elements. Spatial expression profiles revealed that almost all AhCIPKs had tissue-specific expression patterns. Furthermore, association analysis identified one polymorphic site in AdCIPK12 (AhCIPK11), which was significantly associated with pod length, seed length, hundred seed weight, and shoot root ratio. Our results provide valuable information of CIPKs in peanut and facilitate better understanding of their biological functions.

Overexpression of 42 kDa chitinase genes from Trichoderma asperellum SH16 in peanut (Arachis hypogaea)

ABSTRACT In tropical and subtropical areas, peanuts are a very important legume crop that is widely cultivated for food and cooking oil. They are, however, extremely susceptible to a wide range of phytopathogens, particularly soil-borne fungi, which result in low yields and poor seed quality. This study aimed to express three Trichoderma asperellum SH16 42 kDa chitinase-encoding genes in peanut to improve their resistance to some soil-borne fungi. Chi42 is a synthetic, intronless, wild-type gene, whereas syncodChi42-1 and syncodChi42-2 are peanut codon-optimized synthetic genes. These genes were introduced into a local peanut strain through Agrobacterium-mediated transformation. Analysis of the transgenic peanut lines showed that chitinase-specific activities from the syncodChi42-1 and syncodChi42-2 genes were approximately 1.2 and 1.4 times higher than those of the wild-type gene, respectively. The engineered peanut plants also exhibited antifungal activity against the soil-borne pathogenic fungus Sclerotium rolfsii. The transgenic peanut lines transformed with the two synthetic genes have stronger antifungal activities than those transformed with the wild-type version, suggesting that they could be used as novel peanut lines to combat phytopathogenic fungi.

Genome-wide identification and expression analysis of the AhTrx family genes in peanut

Thioredoxins (Trx) are small multifunctional redox proteins that contain thioredoxin conserved domain and active site WCXXC. The Trx family has an important role in multiple processes, including electron transport, seed germination, redox regulation, biotic and abiotic stresses resistance, etc. Although Trx genes have been extensively characterized in some plants, they have not been reported in peanut until now. The identification of AhTrx genes provides potential candidate genes for studying their effects and regulatory mechanisms in peanut (Arachis hypogaea L.) growth and development, especially under aluminium (Al) stress. It is also helpful to further analyze the Al resistance pathway in plants. Seventy AhTrx genes were identified using a genome-wide search method and conservative domain analysis. Then the basic physicochemical properties, phylogenetic relationship, gene structure, chromosomal localization, and promoter prediction were studied by the bioinformatic methods. Furthermore, the expressions of AhTrx genes under different Al treatment times in two peanut cultivars were tested using a real-time quantitative polymerase chain reaction. Seventy AhTrx genes were identified and characterized. Phylogenetic tree analysis showed that all AhTrx members could be classified into 9 groups with different conserved domains. Motif 1 was found to exist in every sequence, with an active site. Furthermore, the gene structures showed that the AhTrx family was complicated and changeable during evolution. The chromosomal localization indicated that the distribution and density of the Trx family on 20 peanut chromosomes were uneven. Predictive promoter analysis indicated that AhTrx proteins might play a role in phytohormones synthesis and stress response. Finally, the expression patterns of the AhTrx genes showed that every gene was differently expressed under Al treatment in different peanut cultivars, some were obvious, others had no significant difference, some were at a high level, while others were at a low level. This study systematically identifies the Trx gene family in peanut, providing some candidates for further study on its effects and regulatory mechanism under Al stress in peanut.

Genome-wide Identification of Metal Tolerance Protein Genes in Peanut: Differential Expression in the Root of Two Contrasting Cultivars Under Metal Stresses.

Metal tolerance proteins (MTP) are Me2+/H+(K+) antiporters that play important roles in the transport of divalent cations in plants. However, their functions in peanut are unknown. In the present study, a total of 24 AhMTP genes were identified in peanut, which were divided into seven groups belonging to three substrate-specific clusters (Zn-CDFs, Zn/Fe-CDFs, and Mn-CDFs). All AhMTP genes underwent whole genome or segmental gene duplication events except AhMTP12. Most AhMTP members within the same subfamily or group generally have similar gene and protein structural characteristics. However, some genes, such as AhMTP1.3, AhMTP2.4, and AhMTP12, showed wide divergences. Most of AhMTP genes preferentially expressed in reproductive tissues, suggesting that these genes might play roles in metal transport during the pod and seed development stages. Excess metal exposure induced expressions for most of AhMTP genes in peanut roots depending on cultivars. By contrast, AhMTP genes in the root of Fenghua 1 were more sensitive to excess Fe, Cd, and Zn exposure than that of Silihong. Stepwise linear regression analysis showed that the percentage of Fe in shoots significantly and positively correlated with the expression of AhMTP4.1, AhMTP9.1, and AhMTPC4.1, but negatively correlated with that of AhMTPC2.1 and AhMTP12. The expression of AhMTP1.1 showed a significant and negative correlation with the percentage of Mn in shoots. The percentage of Zn in shoots was significantly and positively correlated with the expression of AhMTP2.1 but was negatively correlated with that of AhMTPC2.1. The differential responses of AhMTP genes to metal exposure might be, at least partially, responsible for the different metal translocation from roots to shoots between Fenghua 1 and Silihong.

Genetic characterization of flowering and phytochrome genes in peanut (Arachis hypogaea L.) for early maturity.

Peanut (Arachis hypogaea L.) production and cropping pattern is highly influenced by the climatic factors including temperature and rain pattern fluctuations. It is one of the most important cash crop in the rain fed areas of Pakistan and its production, under changing climatic conditions, that can be improved by developing short duration varieties. The present study was based on the molecular characterization of the maturity associated gene families in the peanut under two light conditions. Genomic analysis based on the in silico study of important gene families for early maturity associated attributes like flowering time, their pattern, duration and photoperiodism was done for a comprehensive mapping of maturity related genes. Phytochromes genes Phy A, Phy B and Phy E and flowering genes FT2a, Ft5a and COL2 were selected for in silico characterization for protein based analysis including Multiple Sequence Alignment (MSA), and Neighbor Joining (NJ) tree. MSA and NJ trees of the peanut with Arabidopsis thaliana and Glycine max showed a clear picture of the phylogenetic relationship on the basis of selected gene proteins. Expression profile of phytochrome and flowering genes revealed that photoperiod conditions i.e. short and long days, have great influence on the Phy A, Phy B and Phy E, Ft2a, FT5a and COL2 gene expression pattern. In current study, the relative expression of all studied genes was found higher in short day light condition at flower initiation stage of the plants than in the long light day condition with exception of COL2 gene protein. The molecular characterization based on the in silico study of the particular genes and qPCR based gene expression profiling of the selected genes provided an evidence of the role of these genes and their comparative analysis under two photoperiodic conditions.

Genome-Wide Analysis and Expression Profiles of Ethylene Signal Genes and Apetala2/Ethylene-Responsive Factors in Peanut (Arachis hypogaea L.)

Peanut is an important oil and economic crop widely cultivated in the world. It has special characteristics such as blooming on the ground but bearing fruits underground. During the peg penetrating into the ground, it is subjected to mechanical stress from the soil at the same time. It has been proved that mechanical stress affects plant growth and development by regulating the ethylene signaling-related genes. In this study, we identified some genes related to ethylene signal of peanut, including 10 ethylene sensors, two constitutive triple responses (CTRs), four ethylene insensitive 2 (EIN2s), four ethylene insensitive 3 (EIN3s), six EIN3-binding F-box proteins (EBFs), and 188 Apetala2/ethylene-responsive factors (AP2/ERFs). One hundred and eighty-eight AP2/ERFs were further divided into four subfamilies, 123 ERFs, 56 AP2s, 6 Related to ABI3/VP1 (RAVs), and three Soloists, of them one hundred and seventy AP2/ERF gene pairs were clustered into segmental duplication events in genome of Arachis hypogaea. A total of 134, 138, 97, and 150 AhAP2/ERF genes formed 210, 195, 166, and 525 orthologous gene pairs with Arachis duranensis, Arachis ipaensis, Arabidopsis thaliana, and Glycine max, respectively. Our transcriptome results showed that two EIN3s (Arahy.J729H0 and Arahy.S7XF8N) and one EBFs (Arahy.G4JMEM) were highly expressed when mechanical stress increased. Among the 188 AhAP2/ERF genes, there were 31 genes with the fragments per kilobase of exon model per million mapped fragments (FPKM) ≥ 100 at least one of the 15 samples of Tifrunner. Among them, three AhAP2/ERFs (Arahy.15RATX, Arahy.FAI7YU, and Arahy.452FBF) were specifically expressed in seeds and five AhAP2/ERFs (Arahy.HGAZ7D, Arahy.ZW7540, Arahy.4XS3FZ, Arahy.QGFJ76, and Arahy.AS0C7C) were highly expressed in the tissues, which responded mechanical stress, suggesting that they might sense mechanical stress. Mechanical stress simulation experiment showed that three AhAP2/ERFs (Arahy.QGFJ76, Arahy.AS0C7C, and Arahy.HGAZ7D) were sensitive to mechanical stress changes and they all had the conservative repressor motif (DLNXXP) in the C-terminus, indicated that they might transmit mechanical stress signals through transcriptional inhibition. This study reveals the regulatory landscape of ethylene signal-related genes in peanut, providing valuable information for the mining of target genes for further study.

Global Survey, Expressions and Association Analysis of CBLL Genes in Peanut.

Cystathionine γ-synthase (CGS), methionine γ-lyase (MGL), cystathionine β-lyase (CBL) and cystathionine γ-lyase (CGL) share the Cys_Met_Meta_PP domain and play important roles in plant stress response and development. In this study, we defined the genes containing the Cys_Met_Meta_PP domain (PF01053.20) as CBL-like genes (CBLL). Twenty-nine CBLL genes were identified in the peanut genome, including 12 from cultivated peanut and 17 from wild species. These genes were distributed unevenly at the ends of different chromosomes. Evolution, gene structure, and motif analysis revealed that CBLL proteins were composed of five different evolutionary branches. Chromosome distribution pattern and synteny analysis strongly indicated that whole-genome duplication (allopolyploidization) contributed to the expansion of CBLL genes. Comparative genomics analysis showed that there were three common collinear CBLL gene pairs among peanut, Arabidopsis, grape, and soybean, but no collinear CBLL gene pairs between peanut and rice. The prediction results of cis-acting elements showed that AhCBLLs, AdCBLLs, and AiCBLLs contained different proportions of plant growth, abiotic stress, plant hormones, and light response elements. Spatial expression profiles revealed that almost all AhCBLLs had significantly higher expression in pods and seeds. All AhCBLLs could respond to heat stress, and some of them could be rapidly induced by cold, salt, submergence, heat and drought stress. Furthermore, one polymorphic site in AiCBLL7 was identified by association analysis which was closely associated with pod length (PL), pod width (PW), hundred pod weight (HPW) and hundred seed weight (HSW). The results of this study provide a foundation for further research on the function of the CBLL gene family in peanut.

Unravelling the treasure trove of drought-responsive genes in wild-type peanut through transcriptomics and physiological analyses of root

Peanut is one of the most valuable legumes, grown mainly in arid and semi-arid regions, where its production may be hindered by the lack of water. Therefore, breeding drought tolerant varieties is of great importance for peanut breeding programs around the world. Unlike cultivated peanuts, wild peanuts have greater genetic diversity and are an important source of alleles conferring tolerance/resistance to abiotic and biotic stresses. To decipher the transcriptome changes under drought stress, transcriptomics of roots of highly tolerant Arachis duranensis (ADU) and moderately susceptible A. stenosperma (AST) genotypes were performed. Transcriptome analysis revealed an aggregate of 1465 differentially expressed genes (DEGs), and among the identified DEGs, there were 366 single nucleotide polymorphisms (SNPs). Gene ontology and Mapman analyses revealed that the ADU genotype had a higher number of transcripts related to DNA methylation or demethylation, phytohormone signal transduction and flavonoid production, transcription factors, and responses to ethylene. The transcriptome analysis was endorsed by qRT-PCR, which showed a strong correlation value (R2 = 0.96). Physio-biochemical analysis showed that the drought-tolerant plants produced more osmolytes, ROS phagocytes, and sugars, but less MDA, thus attenuating the effects of drought stress. In addition, three SNPs of the gene encoding transcription factor NFAY (Aradu.YE2F8), expansin alpha (Aradu.78HGD), and cytokinin dehydrogenase 1-like (Aradu.U999X) exhibited polymorphism in selected different genotypes. Such SNPs could be useful for the selection of drought-tolerant genotypes.

Identification of Peanut Aux/IAA Genes and Functional Prediction during Seed Development and Maturation.

Auxin-responsive genes AUX/IAA are important during plant growth and development, but there are few relevant reports in peanut. In this study, 44 AhIAA genes were identified from cultivated peanut, of which 31 genes were expressed in seed at varying degrees. AhIAA-3A, AhIAA-16A and AhIAA-15B were up-regulated, while AhIAA-11A, AhIAA-5B and AhIAA-14B were down-regulated with seed development and maturation. The expression patterns of seven genes, AhIAA-1A, AhIAA-4A, AhIAA-10A, AhIAA-20A, AhIAA-1B, AhIAA-4B and AhIAA-19B, were consistent with the change trend of auxin, and expression in late-maturing variety LM was significantly higher than that in early-maturing EM. Furthermore, allelic polymorphism analysis of AhIAA-1A and AhIAA-1B, which were specifically expressed in seeds, showed that three SNP loci in 3′UTR of AhIAA-1A could effectively distinguish the EM- and LM- type germplasm, providing a basis for breeding markers development. Our results offered a comprehensive understanding of Aux/IAA genes in peanut and provided valuable clues for further investigation of the auxin signal transduction pathway and auxin regulation mechanism in peanut.

Microscopic and Transcriptomic Analyses of Dalbergoid Legume Peanut Reveal a Divergent Evolution Leading to Nod-Factor-Dependent Epidermal Crack-Entry and Terminal Bacteroid Differentiation.

Root nodule symbiosis (RNS) is the pillar behind sustainable agriculture and plays a pivotal role in the environmental nitrogen cycle. Most of the genetic, molecular, and cell-biological knowledge on RNS comes from model legumes that exhibit a root-hair mode of bacterial infection, in contrast to the Dalbergoid legumes exhibiting crack-entry of rhizobia. As a step toward understanding this important group of legumes, we have combined microscopic analysis and temporal transcriptome to obtain a dynamic view of plant gene expression during Arachis hypogaea (peanut) nodule development. We generated comprehensive transcriptome data by mapping the reads to A. hypogaea, and two diploid progenitor genomes. Additionally, we performed BLAST searches to identify nodule-induced yet-to-be annotated peanut genes. Comparison between peanut, Medicago truncatula, Lotus japonicus, and Glycine max showed upregulation of 61 peanut orthologs among 111 tested known RNS-related genes, indicating conservation in mechanisms of nodule development among members of the Papilionoid family. Unlike model legumes, recruitment of class 1 phytoglobin-derived symbiotic hemoglobin (SymH) in peanut indicates diversification of oxygen-scavenging mechanisms in the Papilionoid family. Finally, the absence of cysteine-rich motif-1-containing nodule-specific cysteine-rich peptide (NCR) genes but the recruitment of defensin-like NCRs suggest a diverse molecular mechanism of terminal bacteroid differentiation. In summary, our work describes genetic conservation and diversification in legume-rhizobia symbiosis in the Papilionoid family, as well as among members of the Dalbergoid legumes.[Formula: see text] Copyright © 2022 The Author(s). This is an open access article distributed under the CC BY-NC-ND 4.0 International license.

Genome-wide investigation of defensin genes in peanut (Arachis hypogaea L.) reveals AhDef2.2 conferring resistance to bacterial wilt

Peanut (Arachis hypogea L.) bacterial wilt (BW) is a devastating disease caused by Ralstonia solanacearum that results in severe yield and quality losses. Plant defensins are short cysteine-rich peptides with antimicrobial activity. The role of defensin genes (AhDef) in peanut is unclear. A genome-wide investigation of AhDef genes was undertaken, and 12 identified AhDef genes were classified into two groups containing the gamma-thionin domain formed by four disulfide pairs: Cys1-Cys8, Cys2-Cys5, Cys3-Cys6, and Cys4-Cys7. In silico analysis revealed that AhDef genes showed highly conserved architectural features and contained cis-elements associated with phytohormone signaling and defense responses. A highly resistant cultivar, H108 (R) and a susceptible accession, H107 (S) were tested by R. solanacearum inoculation. H108 (R) showed fewer symptoms than H107 (S) owing to inhibition of bacterial reproduction and spread in the vascular bundles of roots and stems. In a transcriptomic expression profile, AhDef genes, particularly AhDef1.6 and AhDef2.2, were up-regulated in H108 (R) compared with H107 (S) under R. solanacearum infection and phytohormone treatment. Subcellular localization showed that the AhDef1.6 and AhDef2.2 proteins were both expressed specifically on the plasma membrane. Overexpression of protein fusion AhDef2.2-YFP in Nicotiana benthamiana and peanut leaves increased resistance to R. solanacearum, suggesting its role in response to BW infection. AhDef2.2 may be valuable for peanut resistance breeding.

Genome-Wide Identification and Expression Analysis of AP2/ERF Transcription Factor Related to Drought Stress in Cultivated Peanut (Arachis hypogaea L.).

APETALA2/ethylene response element-binding factor (AP2/ERF) transcription factors (TFs) have been found to regulate plant growth and development and response to various abiotic stresses. However, detailed information of AP2/ERF genes in peanut against drought has not yet been performed. Herein, 185 AP2/ERF TF members were identified from the cultivated peanut (A. hypogaea cv. Tifrunner) genome, clustered into five subfamilies: AP2 (APETALA2), ERF (ethylene-responsive-element-binding), DREB (dehydration-responsive-element-binding), RAV (related to ABI3/VP), and Soloist (few unclassified factors)). Subsequently, the phylogenetic relationship, intron–exon structure, and chromosomal location of AhAP2/ERF were further characterized. All of these AhAP2/ERF genes were distributed unevenly across the 20 chromosomes, and 14 tandem and 85 segmental duplicated gene pairs were identified which originated from ancient duplication events. Gene evolution analysis showed that A. hypogaea cv. Tifrunner were separated 64.07 and 66.44 Mya from Medicago truncatula L. and Glycine max L., respectively. Promoter analysis discovered many cis-acting elements related to light, hormones, tissues, and stress responsiveness process. The protein interaction network predicted the exitance of functional interaction among families or subgroups. Expression profiles showed that genes from AP2, ERF, and dehydration-responsive-element-binding subfamilies were significantly upregulated under drought stress conditions. Our study laid a foundation and provided a panel of candidate AP2/ERF TFs for further functional validation to uplift breeding programs of drought-resistant peanut cultivars.

Genetic engineering and genome editing techniques in peanut plants

Research has long been associated with human life. In the effort to make a living, many experts who have contributed to the modernization of traditional research methods by conducting various research activities. In this process, professionals, from farmers to senior researchers, have done their part by developing plants that can tolerate or resist to disease. The growing population, climate change and plant disease are having a devastating effect on food security. In particular, it is essential to increase food production by producing high yielding crops of good quality, that may ensure food security. Recently, different gene- editing technologies have been developed. These techniques have been applied in many research fields and their development has provided economic benefits to farmers. Agrobacterium-mediated and biolistic methods are very important techniques for transforming genetic materials in plants. Genome- editing technologies are recent and highly applied in plant research to improve genes associated with yield, disease resistance and drought resistance. For example, Zinc-finger Nucleases (ZFNS), Transcription Activator-like Effector Nucleases (TALEN), and Clustered Regularly Interspaced Short Palindromic Repeats system (CRISPR/ Cas9) methods are now widely applied by researchers and are playing a positive role in increasing production and productivity. Of the gene- editing technology, CRISPR/ Cas9 is widely applied in plant breeding programme as it is easy to use and cost-effective. In this review, we mainly focus on peanut plant, which is an important oil-bearing allotetraploid crop. Therefore, peanut gene editing-technology could increase the oleic acid content in edible peanut oil. Thus, genome editing and gene transformation technologies are extensively explored in this review.