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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.

Herein we performed bioinformatics analysis of patatin-like protein (PLP) family genes, including gene numbers, gene structure, chromosomal distribution, and expression levels, in order to establish a theoretical foundation for genes encoding PLPs in peanut (Arachis hypogaea L.). In total, 49 PLP family members were identified: 26 in A. hypogaea, 11 in A. duranansis (AA), and 12 in A. ipaensis (BB). They were classified into four categories (class II, III, V and VI), and unevenly distributed on 20 chromosomes. Gene structure analysis revealed that the exon numbers varied from 2 to 14, and the length of amino acid ranged from 157 to 812 aa with isoelectric point (pI) ranged from 4.55 to 8.74. All the PLP family members contained the conserved patatin-like phospholipase domain, but none of them contained signal peptides, and only four contained transmembrane domains. Promoter analysis showed that PLP-encoding genes contained cis-acting regulatory elements related to hormone responses, environmental adaptability and stress response induction. RNA-seq data showed that these genes were expressed under different spatiotemporal conditions. The relative expression levels of PLP-encoding genes in different tissues were detected using quantitative real-time polymerase chain reaction (qRT-PCR). AhPLP1 and AhPLP10 expression levels in flowers were relatively high, while AhPLP4 expression level in roots, stems, and flowers was extremely low, which indicated the potential functions of PLPs in peanut.

Salvia leucantha (Lamiaceae) is an important horticultural plant with great ornamental and economic value. Here, we report the complete chloroplast genome of this species. The chloroplast genome was determined to be 151021 bp and the GC contents was 38.0%. The sequence includes a large single copy (LSC) region of 82,262 bp, a small single copy (SSC) region of 17,537 bp, and two separated inverted regions of 25,611 bp each. It contains 130 unique genes, including 85 protein-coding genes, 37 tRNA genes, and 8 rRNA genes. Based on the chloroplast genomes data of 26 species in Salvia, our result indicated that S. leucantha, S. tiliifolia, S. hispanica, and S. splendens formed one clade with Bootstrap = 100%. The four species belong to Salvia subgenus Calosphace, and S. leucantha was closely related to Salvia tiliifolia and Salvia hispanica. This result will facilitate population, genetic diversity and phylogenetic studies of S. leucantha.

Certain tephritid fruit flies, such as the oriental fruit fly, Bactrocera dorsalis , the Chinese citrus fly, B. minax and the Japanese orange fly, B. tsuneonis (Diptera: Tephritidae: Dacinae), are destructive citrus pests in China. A two-year trapping study was conducted in pomelo, Citrus maxima, groves in Fujian Province of China. The objectives of this study were to investigate the species, the abundance of tephritid fruit flies in the orchards, as well as the efficacy of the selected lure traps to these flies. Four lure traps or devices, i.e. methyl eugenol + Steiner trap (ST), cuelure + ST, ammonium acetate + putrescine + ST, and sticky spheres, were deployed from June to November 2017 and April to October 2018. Six economically significant Dacini pests were trapped during the period. These flies are B. dorsalis, the melon fruit fly, Zeugodacus cucurbitae, the pumpkin fruit fly, Z. tau, the Malaysian fruit fly, B. latifrons, and other two species - B. rubigina and Z. scutellatus. B. dorsalis was the most abundant, accounting for more than 50% of the capture, followed by Z. cucurbitae. The remaining four species accounted for less than 2% of the total capture. B. minax and B. tsuneonis, two destructive citrus-damaging tephritid fruit flies in China, were not found during the trapping period. Methyl eugenol trapped the highest number of fruit flies, followed by cuelure.

BackgroundZhengdan 958 (Zheng 58 × Chang 7–2), a commercial hybrid that is produced in a large area in China, is the result of the successful use of the heterotic pattern of Reid × Tang-SPT. The jointing stage of maize is the key period from vegetative to reproductive growth, which determines development at later stages and heterosis to a certain degree. MicroRNAs (miRNAs) play vital roles in the regulation of plant development, but how they function in the sixth leaf at the six-leaf (V6) stage to influence jointing stage heterosis is still unclear.ResultOur objective was to study miRNAs in four hybrid combinations developed in accordance with the Reid × Tang-SPT pattern, Zhengdan 958, Anyu 5 (Ye 478 × Chang 7–2), Ye 478 × Huangzaosi, Zheng 58 × Huangzaosi, and their parental inbred lines to explore the mechanism related to heterosis. A total of 234 miRNAs were identified in the sixth leaf at the V6 stage, and 85 miRNAs were differentially expressed between the hybrid combinations and their parental inbred lines. Most of the differentially expressed miRNAs were non-additively expressed, which indicates that miRNAs may participate in heterosis at the jointing stage. miR164, miR1432 and miR528 families were repressed in the four hybrid combinations, and some miRNAs, such as miR156, miR399, and miR395 families, exhibited different expression trends in different hybrid combinations, which may result in varying effects on the heterosis regulatory mechanism.ConclusionsThe potential targets of the identified miRNAs are related to photosynthesis, the response to plant hormones, and nutrient use. Different hybrid combinations employ different mature miRNAs of the same miRNA family and exhibit different expression trends that may result in enhanced or repressed gene expression to regulate heterosis. Taken together, our results reveal a miRNA-mediated network that plays a key role in jointing stage heterosis via posttranscriptional regulation.

Background Three-dimensional (3D) chromatin organization provides a critical foundation to investigate gene expression regulation and cellular homeostasis. Results Here, we present the first 3D genome architecture maps in wild type and mutant allotetraploid peanut lines, which illustrate A/B compartments, topologically associated domains (TADs), and widespread chromatin interactions. Most peanut chromosomal arms (52.3%) have active regions (A compartments) with relatively high gene density and high transcriptional levels. About 2.0% of chromosomal regions switch from inactive to active (B-to-A) in the mutant line, harboring 58 differentially expressed genes enriched in flavonoid biosynthesis and circadian rhythm functions. The mutant peanut line shows a higher number of genome-wide cis-interactions than its wild-type. The present study reveals a new TAD in the mutant line that generates different chromatin loops and harbors a specific upstream AP2EREBP-binding motif which might upregulate the expression of the GA2ox gene and decrease active gibberellin (GA) content, presumably making the mutant plant dwarf. Conclusions Our findings will shed new light on the relationship between 3D chromatin architecture and transcriptional regulation in plants.

Seed size/weight, a key domestication trait, is also an important selection target during peanut breeding. However, the mechanisms that regulate peanut seed development are unknown. We re-sequenced 12 RNA samples from developing seeds of two cultivated peanut accessions (Lines 8106 and 8107) and wild Arachis monticola at 15, 30, 45, and 60 days past flowering (DPF). Transcriptome analyses showed that ∼36,000 gene loci were expressed in each of the 12 RNA samples, with nearly half exhibiting moderate (2 ≤ FPKM < 10) expression levels. Of these genes, 12.2% (4,523) were specifically expressed during seed development, mainly at 15 DPF. Also, ∼12,000 genes showed significant differential expression at 30, 45, and/or 60 DPF within each of the three peanut accessions, accounting for 31.8–34.1% of the total expressed genes. Using a method that combined comprehensive transcriptome analysis and previously mapped QTLs, we identified several candidate genes that encode transcription factor TGA7, topless-related protein 2, IAA-amino acid hydrolase ILR1-like 5, and putative pentatricopeptide repeat-containing (PPR) protein. Based on sequence variations identified in these genes, SNP markers were developed and used to genotype both 30 peanut landraces and a genetic segregated population, implying that EVM0025654 encoding a PPR protein may be associated with the increased seed size/weight of the cultivated accessions in comparison with the allotetraploid wild peanut. Our results provide additional knowledge for the identification and functional research into candidate genes responsible for the seed size/weight phenotype in peanut.

Peanut (Arachis hypogaea L.) is an important oilseed and cash crop worldwide. Wild Arachis spp. are potental sources of novel genes for the genetic improvement of cultivated peanut. Understanding the genetic relationships with cultivated peanut is important for the efficient use of wild species in breeding programmes. However, for this genus, only a few genetic resources have been explored so far. In this study, new chloroplast genomic resources have been developed for the genus Arachis based on whole chloroplast genomes from seven species that were sequenced using next-generation sequencing technologies. The chloroplast genomes ranged in length from 156,275 to 156,395 bp, and their gene contents, gene orders, and GC contents were similar to those for other Fabaceae species. Comparative analyses among the seven chloroplast genomes revealed 643 variable sites that included 212 singletons and 431 parsimony-informative sites. We also identified 101 SSR loci and 85 indel mutation events. Thirty-seven SSR loci were found to be polymorphic by in silico comparative analyses. Eleven highly divergent DNA regions, suitable for phylogenetic and species identification, were detected in the seven chloroplast genomes. A molecular phylogeny based on the complete chloroplast genome sequences provided the best resolution of the seven Arachis species.

The oriental fruit fly, Bactrocera dorsalis (Hendel) (Diptera: Tephrtitidae), and the Chinese citrus fly, Bactrocera minax (Enderlein) (Diptera: Tephritidae), are 2 destructive citrus fruit pests in China. A field study was conducted during Sep to Oct of 2018 in Dongkou County of Hunan Province to assess (1) fruit infestations at the time of harvest under 2 management levels, and (2) the efficacy of culling at harvest (i.e., visual inspection and removal of the infested fruits) on reducing the number of infested fruits. A total of 26,400 fruits of Satsuma mandarins, Citrus unshiu (Swingle) Marcov (Rutaceae), were harvested from 2 groves with 1 representing highly managed groves, and the other representing commonly managed groves (low management). Fruit culling was conducted immediately to separate fruits into 5 groups: (1) B. minax infested fruits, (2) B. dorsalis infested fruits, (3) B. minax + B. dorsalis infested fruits, (4) suspected fruit fly infested fruits, and (5) fruit fly free fruits. Fruit dissection was conducted 4 wk later to determine the actual number of the infested fruits, and also to act as a check on the accuracy of visual inspection on the reduction of the number of infested fruits. The highly managed grove had 0.02% infested fruits vs. 2.19% in the low managed grove, a 99.09% reduction in infestation rate. Culling reduced the infested rate to 0.0077% in the highly managed grove and 1.14% in the low managed grove, a reduction of 62% and 48%, respectively, compared to that before culling. About 99% and 73% of fruits which were identified as infested actually were pest free in the 2 groves, respectively. The result of this study suggests that field management is highly effective and critical in reducing fruit fly infestation. The efficacy of culling at harvest on reducing the number of infested fruits was moderate. The accuracy of using culling for identifying the infested fruits was unreliable. Resumo La mosca oriental de la fruta, Bactrocera dorsalis (Hendel) (Diptera: Tephritidae), y la mosca china de los citricos, Bactrocera minax (Enderlein) (Diptera: Tephritidae), son dos plagas destructivas de los citricos en China. Se realizo un estudio de campo durante septiembre a octubre del 2018 en el condado de Dongkou de la provincia de Hunan para evaluar (1) las infestaciones de frutas en el momento de la cosecha bajo 2 niveles de manejo, y (2) la eficacia de la eliminacion selectiva en la cosecha (inspeccion visual y eliminacion de los frutos infestados) sobre la reduccion del numero de frutos infestados. Un total de 26,400 frutos de mandarinas Satsuma, Citrus unshiu (Swingle) Marcov (Rutaceae), fueron recolectados de 2 huertos, con 1 representando huertos sumamente manejados y el otro representando huertos comunmente manejados (bajo manejo). Se separaron las frutas inmediatamente en 5 grupos: (1) frutas infestadas con B. minax, (2) frutas infestadas con B. dorsalis, (3) frutas infestadas con B. minax + B. dorsalis, (4) frutas sospechadas de ser infestadas con moscas de la fruta, y (5) frutas libres de moscas de la fruta. La diseccion de frutos se realizo 4 semanas despues para determinar el numero real de frutos infestados y tambien para actuar como una verificacion de la precision de la inspeccion visual sobre la reduccion del numero de frutos infestados. El huerto sumamente manejado tenia un 0.02% de frutos infestados versus un 2.19% en el huerto comunmente manejado, una reduccion del 99.09% en la tasa de infestacion. El descarte de frutas daňadas redujo la tasa de infestacion al 0,0077% en el huerto sumamente manejado y al 1,14% en el huerto comunmente manejado, una reduccion del 62% y 48%, respectivamente, en comparacion con los niveles antes del descarte de las frutas daňadas. Aproximadamente el 99% y el 73% de las frutas que se identificaron como infestadas en realidad estaban libres de plagas en los 2 huertos, respectivamente. El resultado de este estudio sugiere que el manejo de campo es altamente efectivo y critico para reducir la infestacion de moscas de la fruta. La eficacia del descarte de las frutas daňadas para reducir el numero de frutos infestados fue moderada. La precision de utilizar la seleccion para identificar las frutas infestadas no fue confiable. Key Words: systems approach; Bactrocera minax; Bactrocera dorsalis; fruit dissection; phytosanitary measures View this article in BioOne

Objective Early leaf spot (ELS) caused by Cercospora arachidicola (Hori) is a serious foliar disease in peanut worldwide, which causes considerable reduction of yield. Identification of resistance genes is important for both conventional and molecular breeding. Few resistance genes have been identified and the mechanism of defense responses to this pathogen remains unknown. Results We detected several genes involved in disease resistance to ELS through transcriptome analysis. Using RNA-seq technology, one hundred thirty-three differentially expressed genes (DEGs) were identified between resistant and susceptible lines. Among these DEGs, coiled coil-nucleotide binding-leucine rich repeat (NLR) type resistance genes were identified as duplicated R genes on the chromosome B2. Peanut phytoalexin deficient 4 (PAD4) regulator of effector-triggered immunity mediated by NLR resistance proteins and polyphenol oxidase (PPO) genes play important roles in early leaf spot resistance. Our study provides the useful information on plant response to C. arachidicola infection in peanut. The results suggest that a few major genes and several factors mediate the resistance to ELS disease, showing the characteristics of quantitative trait in defense responses.

Background Long noncoding RNAs (lncRNAs) have several known functions involving various biological regulatory processes in plant. However, the possible roles of lncRNAs during peanut seed development have not been fully explored. Results In this study, two peanut recombinant inbred lines (RIL8) that differ in seed size were used to investigate comprehensive lncRNA profiles derived from the seed development at 15 and 35 days after flowering (DAF). We identified a total of 9388 known and 4037 novel lncRNAs, from which 1437 were differentially expressed lncRNAs. Interestingly, the expression patterns of a number of lncRNAs can be very different between two closely related inbred lines and these lncRNAs were expressed predominantly in only one RIL at 35 DAF. Some differentially expressed lncRNAs were found related to putative cis-acting target genes and predicted to be involved in transcription, transport, cell division, and plant hormone biosynthesis. The expression patterns of several representative lncRNAs and 12 protein-coding genes were validated by qPCR. Same expression pattern was observed between most lncRNAs and their target genes. 11 lncRNAs, XR_001593099.1, MSTRG.18462.1, MSTRG.34915.1, MSTRG.41848.1, MSTRG.22884.1, MSTRG.12404.1, MSTRG.26719.1, MSTRG.35761.1, MSTRG.20033.1, MSTRG.13500.1, and MSTRG.9304.1 and their cis-acting target genes may play key roles in peanut seed development. Conclusions These results provided new information on lncRNA-mediated regulatory roles in peanut seed development, contributing to the comprehensive understanding of the molecular mechanisms involved in peanut seed development.

Metabolomics is an effective biotechnological tool that can be used to attain comprehensive information on metabolites. In this study, the profiles of metabolites produced by wheat seedlings in response to drought stress were investigated using an untargeted approach with ultra-performance liquid chromatography-mass spectrometry (UPLC-MS) to determine various physiological processes related to drought tolerance from the cross between drought-tolerant genotype (HX10) and drought-sensitive genotype (YN211). The current study results showed that under drought stress, HX10 exhibited higher growth indices than YN211. After drought stress treatment, a series of phenolics accumulated higher in HX10 than in YN211, whereas the amount of thymine, a pyrimidine, is almost 13 folds of that in YN211. These metabolites, as well as high levels of different amino acids, alkaloids, organic acids, and flavonoids in the drought treated HX10 could help to explain its strong drought-tolerant capacity. The current study explored the understanding of the mechanisms involved in the drought response of wheat seedling, these metabolome data could also be used for potential QTL or GWAS studies to identify locus (loci) or gene(s) associated with these metabolic traits for the crop improvement.

The Chinese citrus fly, Bactrocera minax (Enderlein) (Diptera: Tephritidae), is the most destructive citrus pest in many citrus production areas in China. The pest is oligophagous, feeding exclusively on the fruits of citrus plants. The pest is univoltine, with adults emerging during April to May and overwintering as pupae. Evidence suggests that the region of origin of the species might be in the elevated temperate southern Yunnan-Guizhou Plateau, spreading out through China’s major waterway systems. Currently, B. minax occurs in nine citrus producing provinces in China, but mostly prominently in the five south central provinces or municipalities of Guizhou, Hubei, Hunan, Sichuan, and Chongqing. Fruit infestations in these provinces are generally moderate to severe. The species is not reported in the four southern citrus production provinces of Guangdong, Fujian, Zhejiang, and Hainan (island). Orchard sanitation such as collection and treatment of the fallen and hanging infested fruits, mass trapping by using various food-based traps with insecticides, and foliar and ground insecticide sprays are the primary pest management options. Sterile insect technology was studied in the field in the 1980s to 1990s, with promising outcomes. The two highly attractive kairomone lures used for many Bactrocera species, cuelure or methyl eugenol, are not attractive to this species. Hydrolyzed protein, sugar and vinegar mixture, and waste brewer's yeast are the most common lures being used in China. Published data indicated that the quality and efficacy of these lures are inconsistent and disputable. Visual cue lures such as colored sticky spheres are also being used in the field. Preliminary field studies suggested that female rectum extracts demonstrated high attraction to males as well as females of the species. Phytosanitary treatment studies in China focus on irradiation and cold treatment. The outcomes of irradiation appeared promising. When B. minax larvae were treated with an irradiation dose of 50 Gy, no adults emerged from the surviving pupae and larvae failed to pupate when the dose reached 70 Gy. No fruit quality was impacted by the treatment. Results from several small-scale cold treatment studies were less promising and inconsistent. One study indicated that under 0°C constant treatment, no mortality of 3rd instar larvae occurred until day 12, and only 55% mortality occurred by day 22. The scientific and technological gaps in safeguarding US citrus industry from the invasion of this destructive pest include: 1) lack of effective lures for early detection and emergency responses; 2) insufficient work on phytosanitary treatment techniques; and 3) weak definition of and lack of data for B. minax pest free areas in China.

Auxin response factors (ARFs) are transcription factors that regulate the expression of auxin response genes, and have important functions in plant growth and development. In this study, available genome data for peanut (Arachis hypogaea L.) were used to identify AhARF genes. In total, 61 AhARFs and 23 AtARFs were divided into six groups (I–VI). Molecular structural analysis revealed that the protein members of AhARF contain at least two domains, the B3 domain and the Auxin-resp domain, and that some have a C-terminal dimerisation domain. Screening of the transcriptome data of 22 tissues of A. hypogaea cv. Tifrunner in a public database showed high expression levels of AhARF2 and AhARF6. AhARF6 was expressed more highly in the stem and branch than in the root and leaf of the wild species Arachis monticola (A. mon) and cultivated species H103. After treatment with exogenous auxin (NAA), the expression of AhARF6 was inhibited, and this inhibition was greater in A. mon than in H103. The transcriptome map revealed that the expression of AhARF6 was higher in the larger pods of H8107 and ZP06 than in the medium pods of H103 and small pods of A. mon. Moreover, AhARF6-5 was proven to be localised in the nucleus, consistent with the location of AtARF6. These results suggest that AhARF6 may play an important role in pod development in peanut.

AbsractPeanut (Arachis hypogaea L.) is an important oilseed and cash crop worldwide. Wild Arachis spp. are potental sources of novel genes for the genetic improvement of cultivated peanut. Understanding the genetic relationships with cultivated peanut is important for the efficient use of wild species in breeding programmes. However, for this genus, only a few genetic resources have been explored so far. In this study, new chloroplast genomic resources have been developed for the genus Arachis based on whole chloroplast genomes from seven species that were sequenced using next-generation sequencing technologies. The chloroplast genomes ranged in length from 156,275 to 156,395 bp, and their gene contents, gene orders, and GC contents were similar to those for other Fabaceae species. Comparative analyses among the seven chloroplast genomes revealed 643 variable sites that included 212 singletons and 431 parsimony-informative sites. We also identified 101 SSR loci and 85 indel mutation events. Thirty-seven SSR loci were found to be polymorphic by in silico comparative analyses. Eleven highly divergent DNA regions, suitable for phylogenetic and species identification, were detected in the seven chloroplast genomes. A molecular phylogeny based on the complete chloroplast genome sequences provided the best resolution of the seven Arachis species.

The wild allotetraploid peanut species Arachis monticola is an important and unique link from the wild diploid species to cultivated tetraploid species in the Arachis lineage. In article number https://doi.org/10.1002/advs.201901672, Dongmei Yin, Jinsong Zhang, Wei Hu, Z. Jeffrey Chen, and co‐workers present a fully‐annotated sequence of the A. monticola genome and comparative genomics of the Arachis species, which reveal asymmetric subgenome evolution and genome‐assisted improvement of peanut production and resistance.

Like many important crops, peanut is a polyploid that underwent polyploidization, evolution, and domestication. The wild allotetraploid peanut species Arachis monticola (A. monticola) is an important and unique link from the wild diploid species to cultivated tetraploid species in the Arachis lineage. However, little is known about A. monticola and its role in the evolution and domestication of this important crop. A fully annotated sequence of ≈2.6 Gb A. monticola genome and comparative genomics of the Arachis species is reported. Genomic reconstruction of 17 wild diploids from AA, BB, EE, KK, and CC groups and 30 tetraploids demonstrates a monophyletic origin of A and B subgenomes in allotetraploid peanuts. The wild and cultivated tetraploids undergo asymmetric subgenome evolution, including homoeologous exchanges, homoeolog expression bias, and structural variation (SV), leading to subgenome functional divergence during peanut domestication. Significantly, SV‐associated homoeologs tend to show expression bias and correlation with pod size increase from diploids to wild and cultivated tetraploids. Moreover, genomic analysis of disease resistance genes shows the unique alleles present in the wild peanut can be introduced into breeding programs to improve some resistance traits in the cultivated peanuts. These genomic resources are valuable for studying polyploid genome evolution, domestication, and improvement of peanut production and resistance., The wild allotetraploid peanut species Arachis monticola (A. monticola) is an important and unique link from the wild diploid species to cultivated tetraploid species in the Arachis lineage. A fully annotated sequence of the A. monticola genome and comparative genomics of Arachis species are presented, which reveals asymmetric subgenome evolution and genome‐assisted improvement of peanut production and resistance.

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

Peanut seeds have a high oil content making them an important oil crop. During development and germination, seeds undergo complex dynamic and physiological changes. Changes in lipid metabolism and underlying mechanisms during seed development have been studied extensively by DNA and RNA sequencing; however, there are few studies on dynamic changes of proteomics during peanut seed development and germination. In this study, proteomic analyses were carried out 20, 40, 60, and 80 days after pollination and 5, 10, 20, and 30 days after germination using isobaric tags for relative and absolute quantitation (iTRAQ) technology to determine the protein profiles of lipid dynamics during peanut seed development and postgermination. A total of 5712 of 8505 proteins were identified, quantified, and divided into 23 functional groups, the largest of which was metabolism-related. Further analyses of the proteins and their pathways revealed initiation of fatty acid accumulation at early stages after flowering, while lipid degradation occurred largely through the lipoxygenase-dependent pathway. Protein expression patterns related to lipid accumulation and degradation were also verified at transcript levels using quantitative real-time polymerase chain reaction. The proteome profiles determined here will significantly enrich our understanding of the process of lipid accumulation and degradation and the dynamic changes in metabolic networks during peanut development.

Arachis monticola (2n = 4x = 40) is the only allotetraploid wild peanut within the Arachis genus and section, with an AABB-type genome of ∼2.7 Gb in size. The AA-type subgenome is derived from diploid wild peanut Arachis duranensis, and the BB-type subgenome is derived from diploid wild peanut Arachis ipaensis. A. monticola is regarded either as the direct progenitor of the cultivated peanut or as an introgressive derivative between the cultivated peanut and wild species. The large polyploidy genome structure and enormous nearly identical regions of the genome make the assembly of chromosomal pseudomolecules very challenging. Here we report the first reference quality assembly of the A. monticola genome, using a series of advanced technologies. The final whole genome of A. monticola is ∼2.62 Gb and has a contig N50 and scaffold N50 of 106.66 Kb and 124.92 Mb, respectively. The vast majority (91.83%) of the assembled sequence was anchored onto the 20 pseudo-chromosomes, and 96.07% of assemblies were accurately separated into AA- and BB- subgenomes. We demonstrated efficiency of the current state of the strategy for de novo assembly of the highly complex allotetraploid species, wild peanut (A. monticola), based on whole-genome shotgun sequencing, single molecule real-time sequencing, high-throughput chromosome conformation capture technology, and BioNano optical genome maps. These combined technologies produced reference-quality genome of the allotetraploid wild peanut, which is valuable for understanding the peanut domestication and evolution within the Arachis genus and among legume crops.

Seed expansion in peanut is a complex biological process involving many gene regulatory pathways. MicroRNAs (miRNAs) play important regulatory roles in plant growth and development, but little is known about their functions during seed expansion, or how they contribute to seed expansion in different peanut lines. We examined seed miRNA expression patterns at 15 and 35 days after flowering (DAF) in two peanut eighth-generation recombinant inbred lines (RIL8); 8106, a medium-pod variety, and 8107, a super-pod variety. Using high-throughput sequencing, we identified 1,082 miRNAs in developing peanut seeds including 434 novel miRNAs. We identified 316 differentially expressed miRNAs by comparing expression levels between the two peanut lines. Interestingly, 24 miRNAs showed contrasting patterns of expression in the two RILs, and 149 miRNAs were expressed predominantly in only one RIL at 35 DAF. Also, potential target genes for some conserved and novel miRNAs were identified by degradome sequencing; target genes were predicted to be involved in auxin mediated signaling pathways and cell division. We validated the expression patterns of some representative miRNAs and 12 target genes by qPCR, and found negative correlations between the expression level of miRNAs and their targets. miR156e, miR159b, miR160a, miR164a, miR166b, miR168a, miR171n, miR172c-5p, and miR319d and their corresponding target genes may play key roles in seed expansion in peanut. The results of our study also provide novel insights into the dynamic changes in miRNAs that occur during peanut seed development, and increase our understanding of miRNA function in seed expansion.

Peanut (Arachis hypogaea) consists of two subspecies, hypogaea and fastigiata, and has been cultivated worldwide for hundreds of years. Here, 158 peanut accessions were selected to dissect the molecular footprint of agronomic traits related to domestication using specific-locus amplified fragment sequencing (SLAF-seq method). Then, a total of 17,338 high-quality single nucleotide polymorphisms (SNPs) in the whole peanut genome were revealed. Eleven agronomic traits in 158 peanut accessions were subsequently analyzed using genome-wide association studies (GWAS). Candidate genes responsible for corresponding traits were then analyzed in genomic regions surrounding the peak SNPs, and 1,429 genes were found within 200 kb windows centerd on GWAS-identified peak SNPs related to domestication. Highly differentiated genomic regions were observed between hypogaea and fastigiata accessions using FST values and sequence diversity (π) ratios. Among the 1,429 genes, 662 were located on chromosome A3, suggesting the presence of major selective sweeps caused by artificial selection during long domestication. These findings provide a promising insight into the complicated genetic architecture of domestication-related traits in peanut, and reveal whole-genome SNP markers of beneficial candidate genes for marker-assisted selection (MAS) in future breeding programs.

It is a long history of theoretical interest in understanding the genetic causes and consequences of shifts between outcrossing and inbreeding in plant mating systems. Selfincompatibility (SI) systems genetically promote outcrossing, and its transitions to inbreeding potentially changes genetic diversity in the evolution of species. SI in the Brassicaceae family is sporophytically controlled by a single locus (S-locus), which locates the female determinant gene SRK (S-locus receptor kinase) and the male determinant gene SCR (S-locus cysteine rich). Operation of diversifying selection maintains the diversity of SRK and SCR during the evolutionary course of S haplotypes. Here we used deduced amino acid sequences of SRK and/or SCR publicly available from seven species in three genera, Brassica, Arabidopsis and Raphanus, to investigate the sequence diversification and phylogenetic distribution of S haplotypes in the Brassicaceae family. The results reveal that SCR shows higher sequence distance than SRK within or between genera, and also in the interspecific pairs of S haplotypes. Phylogenetic analysis supports the conclusion that SI has a single origin but evolves differently within the Brassicaceae. The genetic mechanisms and consequences of the loss of SI in the Brassicaceae family are discussed.

Background MicroRNAs (miRNAs) play critical roles in the processes of plant growth and development, but little is known of their functions during dehydration stress in wheat. Moreover, the mechanisms by which miRNAs confer different levels of dehydration stress tolerance in different wheat genotypes are unclear. Results We examined miRNA expressions in two different wheat genotypes, Hanxuan10, which is drought-tolerant, and Zhengyin1, which is drought-susceptible. Using a deep-sequencing method, we identified 367 differentially expressed miRNAs (including 46 conserved miRNAs and 321 novel miRNAs) and compared their expression levels in the two genotypes. Among them, 233 miRNAs were upregulated and 10 were downregulated in both wheat genotypes after dehydration stress. Interestingly, 13 miRNAs exhibited opposite patterns of expression in the two wheat genotypes, downregulation in the drought-tolerant cultivar and upregulation in the drought-susceptible cultivar. We also identified 111 miRNAs that were expressed predominantly in only one or the other genotype after dehydration stress. We verified the expression patterns of a number of representative miRNAs using qPCR analysis and northern blot, which produced results consistent with those of the deep-sequencing method. Moreover, monitoring the expression levels of 10 target genes by qPCR analysis revealed negative correlations with the levels of their corresponding miRNAs. Conclusions These results indicate that differentially expressed patterns of miRNAs between these two genotypes may play important roles in dehydration stress tolerance in wheat and may be a key factor in determining the levels of stress tolerance in different wheat genotypes. Electronic supplementary material The online version of this article (doi:10.1186/s12870-015-0413-9) contains supplementary material, which is available to authorized users.

Part 1: Decision Support Systems, Intelligent Systems and Artificial Intelligence Applications; International audience; The solanum fruit fly, Bactrocera latifrons (Hendel), is a major pest throughout South and South East Asia, including very few parts of southern China, and has invaded Hawaii and recently the continent of Africa (Tanzania and Kenya). With the development of international trade in fruits and vegetables, B. latifrons has become a potential threat to Chinese agriculture. In this study, CLIMEX 3.0 and ArcGIS 9.3 were used to predict the current and future potential geographical distribution of B. latifrons in China. Under current climatic conditions, its projected potential distribution includes most parts of southern China (about 32.2% of all 748 meteorological stations), from 16.544°N to 32.442°N. Optimal climate conditions occur in most areas of Yunnan, Guizhou, Sichuan, Chongqing, Hunan, Hubei, Jiangxi, Zhejiang, Fujian, Guangdong, Guangxi, Hainan, Taiwan, Hong Kong and Macao. The factors limiting the boundary of its suitability range are mainly the cold and dry stress. Climate change scenario for the 2020s indicates that the future potential geographical distribution will be increased by 5% of the total land areas of China, and the northern distribution boundary will move from 32.442°N to 33.408°N. There are 34 non-suitable climate sites change into suitable, mainly in Jiangsu, Anhui, Henan, Shanxi, Gansu, Sichuan and Tibet, because of China is likely to become hotter and wetter in the 2020s. In order to prevent the introduction and spread of B. latifrons, the present plant quarantine and monitor measures should be enhanced more where are projected to be suitable areas under current as well as future climatic conditions. At the same time, we should strengthen education for the public’s awareness of plant protection.