The auxin response factor gene family in banana: genome-wide identification and expression analyses during development, ripening, and abiotic stress

MaC2H2-IDD regulates fruit softening and involved in softening disorder induced by cold stress in banana

Chilling stress causes banana fruit softening disorder and severely impairs fruit quality. Various factors, such as transcription factors, regulate fruit softening. Herein, we identified a novel regulator, MaC2H2-IDD, whose expression is closely associated with fruit ripening and softening disorder. MaC2H2-IDD is a transcriptional activator located in the nucleus. The transient and ectopic overexpression of MaC2H2-IDD promoted "Fenjiao" banana and tomato fruit ripening. However, transient silencing of MaC2H2-IDD repressed "Fenjiao" banana fruit ripening. MaC2H2-IDD modulates fruit softening by activating the promoter activity of starch (MaBAM3, MaBAM6, MaBAM8, MaAMY3, and MaISA2) and cell wall (MaEXP-A2, MaEXP-A8, MaSUR14-like, and MaGLU22-like) degradation genes. DLR, Y1H, EMSA, and ChIP-qPCR assays validated the expression regulation. MaC2H2-IDD interacts with MaEBF1, enhancing the regulation of MaC2H2-IDD to MaAMY3, MaEXP-A2, and MaGLU22-like. Overexpressing/silencing MaC2H2-IDD in banana and tomato fruit altered the transcript levels of the cell wall and starch (CWS) degradation genes. Several differentially expressed genes (DEGs) were authenticated between the overexpression and control fruit. The DEGs mainly enriched biosynthesis of secondary metabolism, amino sugar and nucleotide sugar metabolism, fructose and mannose metabolism, starch and sucrose metabolism, and plant hormones signal transduction. Overexpressing MaC2H2-IDD also upregulated protein levels of MaEBF1. MaEBF1 does not ubiquitinate or degrade MaC2H2-IDD. These data indicate that MaC2H2-IDD is a new regulator of CWS degradation in "Fenjiao" banana and cooperates with MaEBF1 to modulate fruit softening, which also involves the cold softening disorder.

Genomic survey and expression analysis of LcARFs reveal multiple functions to somatic embryogenesis in Liriodendron

BACKGROUND

Auxin response factors (ARFs) are critical transcription factors that mediate the auxin signaling pathway and are essential for regulating plant growth. However, there is a lack of understanding regarding the ARF gene family in Liriodendron chinense, a vital species in landscaping and economics. Thus, further research is needed to explore the roles of ARFs in L. chinense and their potential applications in plant development.

RESULT

In this study, we have identified 20 LcARF genes that belong to three subfamilies in the genome of L. chinense. The analysis of their conserved domains, gene structure, and phylogeny suggests that LcARFs may be evolutionarily conserved and functionally similar to other plant ARFs. The expression of LcARFs varies in different tissues. Additionally, they are also involved in different developmental stages of somatic embryogenesis. Overexpression of LcARF1, LcARF2a, and LcARF5 led to increased activity within callus. Additionally, our promoter-GFP fusion study indicated that LcARF1 may play a role in embryogenesis. Overall, this study provides insights into the functions of LcARFs in plant development and embryogenesis, which could facilitate the improvement of somatic embryogenesis in L. chinense.

CONCLUSION

The research findings presented in this study shed light on the regulatory roles of LcARFs in somatic embryogenesis in L. chinense and may aid in accelerating the breeding process of this tree species. By identifying the specific LcARFs involved in different stages of somatic embryogenesis, this study provides a basis for developing targeted breeding strategies aimed at optimizing somatic embryogenesis in L. chinense, which holds great potential for improving the growth and productivity of this economically important species.

The Zinc Finger Protein MaCCCH33-Like2 Positively Regulates Banana Fruit Ripening by Modulating Genes in Starch and Cell Wall Degradation

As zinc finger protein transcription factors (TFs), the molecular mechanism of Cys-Cys-Cys-His (CCCH) TFs in regulating plant development, growth and stress response has been well studied. However, the roles of CCCH TFs in fruit ripening are still obscure. Herein, we report that MaCCCH33-like2 TF and its associated proteins modulate the fruit softening of 'Fenjiao' bananas. MaCCCH33-like2 interacts directly with the promoters of three genes: isoamylase2 (MaISA2), sugar transporter14-like (MaSUR14-like) and β-d-xylosidase23 (MaXYL23), all of which are responsible for encoding proteins involved in the degradation of starch and cell wall components. Additionally, MaCCCH33-like2 forms interactions with abscisic acid-insensitive 5 (ABI5)-like and ethylene F-box protein 1 (MaEBF1), resulting in enhanced binding and activation of promoters of genes related to starch and cell wall degradation. When MaCCCH33-like2 is transiently and ectopically overexpressed in 'Fenjiao' banana and tomato fruit, it facilitates softening and ripening processes by promoting the degradation of cell wall components and starch and the production of ethylene. Conversely, the temporary silencing of MaCCCH33-like2 using virus-induced gene silencing (VIGS) inhibits softening and ripening in the 'Fenjiao' banana by suppressing ethylene synthesis, as well as starch and cell wall degradation. Furthermore, the promoter activity of MaCCCH33-like2 is regulated by MaABI5-like. Taken together, we have uncovered a novel MaCCCH33-like2/MaEBF1/MaABI5-like module that participates in fruit softening regulation in bananas.

NIT24 and NIT29-mediated IAA synthesis of Xanthomonas oryzae pv. oryzicola suppresses immunity and boosts growth in rice

Auxin plays a pivotal role in the co-evolution of plants and microorganisms. Xanthomonas oryzae pv. oryzicola (Xoc) stands as a significant factor that affects rice yield and quality. However, the current understanding of Xoc's capability for indole 3-acetic acid (IAA) synthesis and its mechanistic implications remains elusive. In this study, we performed a comprehensive genomic analysis of Xoc strain RS105, leading to the identification of two nitrilase enzyme family (NIT) genes, designated as AKO15524.1 and AKO15829.1, subsequently named NIT24 and NIT29, respectively. Our investigation unveiled that the deletion of NIT24 and NIT29 resulted in a notable reduction in IAA synthesis capacity within RS105, thereby impacting extracellular polysaccharide production. This deficiency was partially ameliorated through exogenous IAA supplementation. The study further substantiated that NIT24 and NIT29 have nitrilase activity and the ability to catalyse IAA production in vitro. The lesion length and bacterial population statistics experiments confirmed that NIT24 and NIT29 positively regulated the pathogenicity of RS105, suggesting that NIT24 and NIT29 may regulate Xoc invasion by affecting IAA synthesis. Furthermore, our analysis corroborated mutant strains, RS105_ΔNIT24 and RS105_ΔNIT29, which elicited the outbreak of reactive oxygen species, the deposition of callose and the upregulation of defence-related gene expression in rice. IAA exerted a significant dampening effect on the immune responses incited by these mutant strains in rice. In addition, the absence of NIT24 and NIT29 affected the growth-promoting effect of Xoc on rice. This implies that Xoc may promote rice growth by secreting IAA, thus providing a more suitable microenvironment for its own colonization. In summary, our study provides compelling evidence for the existence of a nitrilase-dependent IAA biosynthesis pathway in Xoc. IAA synthesis-related genes promote Xoc colonization by inhibiting rice immune defence response and affecting rice growth by increasing IAA content in Xoc.

Genome-wide survey, molecular evolution and expression analysis of Auxin Response Factor (ARF) gene family indicating their key role in seed number per pod in pigeonpea (C. cajan L. Millsp.)

Auxin Response Factors (ARF) are a family of transcription factors that mediate auxin signalling and regulate multiple biological processes. Their crucial role in increasing plant biomass/yield influenced this study, where a systematic analysis of ARF gene family was carried out to identify the key proteins controlling embryo/seed developmental pathways in pigeonpea. A genome-wide scan revealed the presence of 12 ARF genes in pigeonpea, distributed across the chromosomes 1, 3, 4, 8 and 11. Domain analysis of ARF proteins showed the presence of B3 DNA binding, AUX response, and IAA domains. Majority of them are of nuclear origin, and do not exhibit the level of genomic expansion as observed in Glycine max (51 members). The duplication events seem to range from 31.6 to 42.3 million years ago (mya). Promoter analysis revealed the presence of multiple cis-acting elements related to stress responses, hormone signalling and other development processes. The expression atlas data highlighted the expression of CcARF8 in hypocotyl, bud and flower whereas, CcARF7 expression was significantly high in pod. The real-time expression of CcARF2, CcARF3 and CcARF18 was highest in genotypes with high seed number indicating their key role in regulating embryo development and determining seed set in pigeonpea.

MaBEL1 regulates banana fruit ripening by activating cell wall and starch degradation-related genes

Banana is a typical subtropical fruit, sensitive to chilling injuries and prone to softening disorder. However, the underlying regulatory mechanisms of the softening disorder caused by cold stress remain obscure. Herein, we found that BEL1-LIKE HOMEODOMAIN transcription factor 1 (MaBEL1) and its associated proteins regulate the fruit softening and ripening process. The transcript and protein levels of MaBEL1 were up-regulated with fruit ripening but severely repressed by the chilling stress. Moreover, the MaBEL1 protein interacted directly with the promoters of the cell wall and starch degradation-related genes, such as MaAMY3, MaXYL32, and MaEXP-A8. The transient overexpression of MaBEL1 alleviated fruit chilling injury and ripening disorder caused by cold stress and promoted fruit softening and ripening of "Fenjiao" banana by inducing ethylene production and starch and cell wall degradation. The accelerated ripening was also validated by the ectopic overexpression in tomatoes. Conversely, MaBEL1-silencing aggravated the chilling injury and ripening disorder and repressed fruit softening and ripening by inhibiting ethylene production and starch and cell wall degradation. MaABI5-like and MaEBF1, the two positive regulators of the fruit softening process, interacted with MaBEL1 to enhance the promoter activity of the starch and cell wall degradation-related genes. Moreover, the F-box protein MaEBF1 does not modulate the degradation of MaBEL1, which regulates the transcription of MaABI5-like protein. Overall, we report a novel MaBEL1-MaEBF1-MaABI5-like complex system that mediates the fruit softening and ripening disorder in "Fenjiao" bananas caused by cold stress.

Genome-wide identification and expression analysis of the Auxin-Response factor (ARF) gene family in Medicago sativa under abiotic stress

BACKGROUND

Alfalfa (Medicago sativa) is the most widely planted legume forage and one of the most economically valuable crops in the world. The periodic changes in its growth and development and abiotic stress determine its yield and economic benefits. Auxin controls many aspects of alfalfa growth by regulating gene expression, including organ differentiation and stress response. Auxin response factors (ARF) are transcription factors that play an essential role in auxin signal transduction and regulate the expression of auxin-responsive genes. However, the function of ARF transcription factors is unclear in autotetraploid-cultivated alfalfa.

RESULT

A total of 81 ARF were identified in the alfalfa genome in this study. Gene Ontology (GO) terms and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathways were analyzed, identifying that ARF genes are mainly involved in transcriptional regulation and plant hormone signal transduction pathways. Phylogenetic analysis showed that MsARF was divided into four clades: I, II, III, and IV, each containing 52, 13, 7, and 9 genes, respectively. The promoter region of the MsARF gene contained stress-related elements, such as ABRE, TC-rich repeats, MBS, LTR. Proteins encoded by 50 ARF genes were localized in the nucleus without guide peptides, signal peptides, or transmembrane structures, indicating that most MsARF genes are not secreted or transported but only function in the nucleus. Protein structure analysis revealed that the secondary and tertiary structures of the 81 MsARF genes varied. Chromosomal localization analysis showed 81 MsARF genes were unevenly distributed on 25 chromosomes, with the highest distribution on chromosome 5. Furthermore, 14 segmental duplications and two sets of tandem repeats were identified. Expression analysis indicated that the MsARF was differentially expressed in different tissues and under various abiotic stressors. The quantitative reverse transcription polymerase chain reaction (qRT-PCR) analysis showed that the expression profiles of 23 MsARF genes were specific to abiotic stresses such as drought, salt, high temperature, and low temperature, as well as tissue-specific and closely related to the duration of stress.

CONCLUSION

This study identified MsARF in the cultivated alfalfa genome based on the autotetraploid level, which GO, KEGG analysis, phylogenetic analysis, sequence characteristics, and expression pattern analysis further confirmed. Together, these findings provide clues for further investigation of MsARF functional verification and molecular breeding of alfalfa. This study provides a novel approach to systematically identify and characterize ARF transcription factors in autotetraploid cultivated alfalfa, revealing 23 MsARF genes significantly involved in response to various stresses.

The Knockdown of AUXIN RESPONSE FACTOR 2 Confers Enhanced Tolerance to Salt and Drought Stresses in Tomato (Solanum lycopersicum L.)

Auxin response factors (ARFs) act as key elements of the auxin-signaling pathway and play important roles in the process of a plant's growth, development, and response to environmental conditions. We studied the implication of the SlARF2 gene in the tomato response to salt (150 mM of NaCl) and drought (15% PEG 20000) stresses. The functional characterization of SlARF2 knockdown tomato mutants revealed that the downregulation of this gene enhanced primary root length and root branching and reduced plant wilting. At the physiological level, the arf2 mutant line displayed higher chlorophyll, soluble sugars, proline, and relative water contents as well as lower stomatal conductance and a decreased malondialdehyde content. Moreover, SlARF2 knockdown tomato mutants demonstrated higher activities of the antioxidant enzymes superoxide dismutase (SOD) and catalase (CAT) under salt and drought stresses than the wild type. Indeed, the stress tolerance of the arf2 mutant was also reflected by the upregulation of stress-related genes involved in ROS scavenging and plant defense, including SOD, CAT, dehydration-responsive element-binding protein, and early responsive to dehydration, which can ultimately result in a better resistance to salt and drought stresses. Furthermore, the transcriptional levels of the Δ1-pyrroline-5-carboxylate synthase (P5CS) gene were upregulated in the arf2 mutant after stress, in correlation with the higher levels of proline. Taken together, our findings reveal that SlARF2 is implicated in salt and drought tolerance in tomato and provides some considerable elements for improving the abiotic stress tolerance and increasing the crop yields of tomato.

Comparative protein analysis of two maize genotypes with contrasting tolerance to low temperature

BACKGROUND

Low temperature (LT) stress is one of the major environmental stress factors affecting the growth and yield of maize (Zea mays L.). Hence, it is important to unravel the molecular mechanisms behind LT stress tolerance to improve molecular breeding in LT tolerant genotypes. In the present study, two maize genotypes viz. Gurez local from Kashmir Himalaya and tropical grown GM6, were dissected for their LT stress response in terms of accumulation of differentially regulated proteins (DRPs). Leaf proteome analysis at three-leaf stage of maize seedlings subjected to LT stress of 6 °C for a total of 12 h duration was performed using two dimensional gel electrophoresis (2D-PAGE) followed by subsequent identification of the proteins involved.

RESULTS

After MALDI-TOF (Matrix-assisted laser desorption/ionization-time of flight) and bioinformatics analysis, 19 proteins were successfully identified in Gurez local, while as 10 proteins were found to get successful identification in GM6. The interesting observations from the present investigation is the identification of three novel proteins viz. threonine dehydratase biosynthetic chloroplastic, thylakoidal processing peptidase 1 chloroplastic, and nodulin-like protein, whose role in abiotic stress tolerance, in general, and LT stress, in particular, has not been reported so far. It is important to highlight here that most of LT responsive proteins including the three novel proteins were identified from Gurez local only, owing to its exceptional LT tolerance. From the protein profiles, obtained in both genotypes immediately after LT stress perception, it was inferred that stress responsive protein accumulation and their expression fashion help the Gurez local in seedling establishment and withstand unfavorable conditions as compared to GM6. This was inferred from the findings of pathway enrichment analysis like regulation of seed growth, timing of floral transition, lipid glycosylation, and aspartate family amino acid catabolic processes, besides other key stress defense mechanisms. However, in GM6, metabolic pathways enriched were found to be involved in more general processes including cell cycle DNA replication and regulation of phenylpropanoid metabolism. Furthermore, majority of the qRT-PCR results of the selected proteins demonstrated positive correlation between protein levels and transcript abundance, thereby strengthening our findings.

CONCLUSIONS

In conclusion, our findings reported majority of the identified proteins in Gurez local exhibiting up-regulated pattern under LT stress as compared to GM6. Furthermore, three novel proteins induced by LT stress were found in Gurez local, requiring further functional validation. Therefore, our results offer more insights for elucidating the molecular networks mediating LT stress tolerance in maize.

Identification and expression of the CCO family during development, ripening and stress response in banana

Plant hormone abscisic acid (ABA) plays an important role in plant growth, development and response to biotic / abiotic stressors. Thus, it is necessary to investigate the crucial genes associated with ABA synthesis. Currently, the carotenoid cleavage oxygenases (CCOs) family that function as the key step for ABA synthesis are not well understood in banana. In this study, 13 MaCCO genes and 12 MbCCO genes, divided into NCED subgroup and CCD subgroup, were identified from the banana genome, and their evolutionary relationship, protein motifs, and gene structures were also determined. Transcriptomic analysis suggested the involvement of CCO genes in banana development, ripening, and response to abiotic and biotic stressors, and homologous gene pairs showed homoeologue expression bias in the A or B subgenome. Our results identified MaNCED3A, MaCCD1, and MbNCED3B as the genes with the highest expression during fruit development and ripening. MaNCED5 / MbNCED5 and MaNCED9A might respond to abiotic stress, and MaNCED3A, 3B, 6 A, 9 A, and MbNCED9A showed transcriptional changes that could be a response to Foc4 infection. These findings may contribute to the characterization of key enzymes involved in ABA biosynthesis, as well as to identify potential targets for the genetic improvement of banana.

MaC2H2-like regulates chilling stress response of ‘Fenjiao’ banana by modulating flavonoid synthesis and fatty acid desaturation

Chilling injury (CI) is a major problem that affects fruit quality and ripening. Herein, chilling stress severely inhibited the expression of transcription factor MaC2H2-like. MaC2H2-like activates the expression of genes associated with flavonoid synthesis (MaC4H-like1, Ma4CL-like1, MaFLS, and MaFLS3) and fatty acid desaturation (MaFAD6-2 and MaFAD6-3), the leading indicators of chilling tolerance. MaC2H2-like interacts with MaEBF1 and boosts the transcriptional activity of MaFAD6-2, MaFAD6-3, Ma4CL-like1, and MaFLS. The overexpression of MaC2H2-like reduced fruit CI, induced the expression of these genes and increased the content of flavonoid and unsaturated fatty acid. Meanwhile, the silencing of MaC2H2-like increased fruit CI and downregulated the expression of those genes and reduced the content of flavonoid and unsaturated fatty acid. These results indicate that MaC2H2-like function as new player in modulating fruit CI by regulating flavonoid synthesis and fatty acid desaturation. MaC2H2-like could be a useful candidate gene for improving cold tolerance in 'Fenjiao' banana.

Genome-Wide Identification and Characterization of Auxin Response Factor (ARF) Gene Family Involved in Wood Formation and Response to Exogenous Hormone Treatment in Populus trichocarpa

Auxin is a key regulator that virtually controls almost every aspect of plant growth and development throughout its life cycle. As the major components of auxin signaling, auxin response factors (ARFs) play crucial roles in various processes of plant growth and development. In this study, a total of 35 PtrARF genes were identified, and their phylogenetic relationships, chromosomal locations, synteny relationships, exon/intron structures, cis-elements, conserved motifs, and protein characteristics were systemically investigated. We also analyzed the expression patterns of these PtrARF genes and revealed that 16 of them, including PtrARF1, 3, 7, 11, 13-17, 21, 23, 26, 27, 29, 31, and 33, were preferentially expressed in primary stems, while 15 of them, including PtrARF2, 4, 6, 9, 10, 12, 18-20, 22, 24, 25, 28, 32, and 35, participated in different phases of wood formation. In addition, some PtrARF genes, with at least one cis-element related to indole-3-acetic acid (IAA) or abscisic acid (ABA) response, responded differently to exogenous IAA and ABA treatment, respectively. Three PtrARF proteins, namely PtrARF18, PtrARF23, and PtrARF29, selected from three classes, were characterized, and only PtrARF18 was a transcriptional self-activator localized in the nucleus. Moreover, Y2H and bimolecular fluorescence complementation (BiFC) assay demonstrated that PtrARF23 interacted with PtrIAA10 and PtrIAA28 in the nucleus, while PtrARF29 interacted with PtrIAA28 in the nucleus. Our results provided comprehensive information regarding the PtrARF gene family, which will lay some foundation for future research about PtrARF genes in tree development and growth, especially the wood formation, in response to cellular signaling and environmental cues.

Characterization and expression analysis of basic leucine zipper (bZIP) transcription factors responsive to chilling injury in peach fruit

BACKGROUND

Peach (Prunus persica L.) is prone to chilling injury as exhibited by inhibition of the ethylene production, failure in softening, and the manifestation of internal browning. The basic leucine zipper (bZIP) transcription factors play an essential role in regulatory networks that control many processes associated with physiological, abiotic and biotic stress responses in fruits. Formerly, the underlying molecular and regulatory mechanism of (bZIP) transcription factors responsive to chilling injury in peach fruit is still elusive.

METHODS AND RESULTS

In the current experiment, the solute peach 'Zhongyou Peach No. 13' was used as the test material and cold storage at low temperature (4 °C). It was found that long-term low-temperature storage induced the production of ethylene, the hardness of the pulp decreased, and the low temperature also induced ABA accumulation. The changes of ABA and ethylene in peach fruits during low-temperature storage were clarified. Since the bZIP transcription factor is involved in the regulation of downstream pathways of ABA signals, 47 peach bZIP transcription factor family genes were identified through bioinformatics analysis. Further based on RT-qPCR analysis, 18 PpbZIP genes were discovered to be expressed in refrigerated peach fruits. Among them, the expression of PpbZIP23 and PpbZIP25 was significantly reduced during the refrigeration process, the promoter analysis of these genes found that this region contains the MYC/MYB/ABRES binding element, but not the DRES/CBFS element, indicating that the expression may be regulated by the ABA-dependent cold induction pathway, thereby responding to chilling injury in peach fruit.

CONCLUSIONS

Over investigation will provide new insights for further postharvest protocols related to molecular changes during cold storage and will prove a better cope for chilling injury.

Genome-wide identification, characterization, and evolutionary analysis of NBS genes and their association with disease resistance in Musa spp

Banana is an important food crop that is susceptible to a wide range of pests and diseases that can reduce yield and quality. The primary objective of banana breeding programs is to increase disease resistance, which requires the identification of resistance (R) genes. Despite the fact that resistant sources have been identified in bananas, the genes, particularly the nucleotide-binding site (NBS) family, which play an important role in protecting plants against pathogens, have received little attention. As a result, this study included a thorough examination of the NBS disease resistance gene family's classification, phylogenetic analysis, genome organization, evolution, cis-elements, differential expression, regulation by microRNAs, and protein-protein interaction. A total of 116 and 43 putative NBS genes from M. acuminata and M. balbisiana, respectively, were identified and characterized, and were classified into seven sub-families. Structural analysis of NBS genes revealed the presence of signal peptides, their sub-cellular localization, molecular weight and pI. Eight commonly conserved motifs were found, and NBS genes were unevenly distributed across multiple chromosomes, with the majority of NBS genes being located in chr3 and chr1 of the A and B genomes, respectively. Tandem duplication occurrences have helped bananas' NBS genes spread throughout evolution. Transcriptome analysis of NBS genes revealed significant differences in expression between resistant and susceptible cultivars of fusarium wilt, eumusae leaf spot, root lesion nematode, and drought, implying that they can be used as candidate resistant genes. Ninety miRNAs were discovered to have targets in 104 NBS genes from the A genome, providing important insights into NBS gene expression regulation. Overall, this study offers a valuable genomic resource and understanding of the function and evolution of NBS genes in relation to rapidly evolving pathogens, as well as providing breeders with selection targets for fast-tracking breeding of banana varieties with more durable resistance to pathogens.

Ethylene Response Factor MaERF012 Modulates Fruit Ripening by Regulating Chlorophyll Degradation and Softening in Banana

Ethylene response factors (ERFs) are one of largest plant-specific transcription factor families involved in fruit ripening. However, the regulatory mechanism by which ERFs modulate fruit yellowing and softening remains unknown in banana. We previously found that the transcription of MaERF012 was closely related to 'Fenjiao' banana fruit ripening. Herein, we found that MaERF012 was differentially expressed in the fruit pulp and peel and was closely related to fruit ripening. MaERF012 activated the promoter activity of one chlorophyll degradation gene (MaSGR1), two starch degradation genes (MaGWD1 and MaAMY3), and three cell wall degradation genes (MaPL8, MaEXP-A8, and MaXYL23-like), which were tested by EMSA, Y1H, and DLR. Transient overexpression of MaERF012 accelerates fruit ripening by promoting fruit yellowing and softening by up-regulating the transcription of chlorophyll, starch, and cell wall degradation genes. Over-expression of MaERF012 alters the transcriptome profiles of the fruit peel and pulp, and the differentially expressed genes were mainly enriched in starch and sucrose metabolism, plant hormone signal transduction, biosynthesis of secondary metabolism, and fructose and mannose metabolism. Overall, the data showed that MaERF012 acts as a transcriptional activator by regulating fruit ripening by activating the transcription of chlorophyll, starch, and cell wall degradation genes.

The banana genome hub: a community database for genomics in the Musaceae

The Banana Genome Hub provides centralized access for genome assemblies, annotations, and the extensive related omics resources available for bananas and banana relatives. A series of tools and unique interfaces are implemented to harness the potential of genomics in bananas, leveraging the power of comparative analysis, while recognizing the differences between datasets. Besides effective genomic tools like BLAST and the JBrowse genome browser, additional interfaces enable advanced gene search and gene family analyses including multiple alignments and phylogenies. A synteny viewer enables the comparison of genome structures between chromosome-scale assemblies. Interfaces for differential expression analyses, metabolic pathways and GO enrichment were also added. A catalogue of variants spanning the banana diversity is made available for exploration, filtering, and export to a wide variety of software. Furthermore, we implemented new ways to graphically explore gene presence-absence in pangenomes as well as genome ancestry mosaics for cultivated bananas. Besides, to guide the community in future sequencing efforts, we provide recommendations for nomenclature of locus tags and a curated list of public genomic resources (assemblies, resequencing, high density genotyping) and upcoming resources-planned, ongoing or not yet public. The Banana Genome Hub aims at supporting the banana scientific community for basic, translational, and applied research and can be accessed at https://banana-genome-hub.southgreen.fr.

Role of MaABI5-like in abscisic acid-induced cold tolerance of 'Fenjiao' banana fruit

Abscisic acid (ABA) is a phytohormone essential for plants to respond to various environmental stresses, and abscisic acid-insensitive 5 (ABI5) is a basic leucine zipper transcription factor of the ABA signaling pathway. Exogenous ABA induces cold tolerance in bananas; however, the role of MaABI5-like in ABA-induced cold tolerance remains unexplored. The present study found that exogenous ABA alleviated chilling injury of 'Fenjiao' banana, induced the accumulation of endogenous ABA, unsaturated fatty acids, and flavonoid content, and reduced the saturated fatty acid content. Moreover, ABA treatment upregulated the transcription levels of MaABI5-like, fatty acid desaturation genes, and flavonoid synthesis-related genes during cold storage. More interestingly, MaABI5-like directly interacted with the promoter of genes related to fatty acid desaturation (MaFAD3-1, MaFAD3-4, MaFAD3-5, MaFAD6-2, MaFAD6-3) and flavonoid synthesis (MaPAL-like, MaPAL-like1, MaC4H-like3, Ma4CL-like1, Ma4CL-like10, MaCHS6-4-like, and MaFLS) and activated their expressions. Furthermore, the transient overexpression of MaABI5-like in 'Fenjiao' banana fruit and ectopic expression in tomato plants enhanced cold tolerance and upregulated fatty acid desaturation and flavonoid synthesis-related gene transcript levels. The reduced expression of MaABI5-like by virus-induced gene silencing in 'Fenjiao' banana increased chilling injury and downregulated the expression of fatty acid desaturation and flavonoid synthesis-related genes. Thus, the study indicates that MaABI5-like regulates ABA-induced cold tolerance by increasing unsaturated fatty acid and flavonoid content.

Small RNA and Degradome Deep Sequencing Reveals the Roles of microRNAs in Peanut (Arachis hypogaea L.) Cold Response

Cold stress is a major environmental factor that affects plant growth and development, as well as fruit postharvest life and quality. MicroRNAs (miRNAs) are a class of non-coding small RNAs that play crucial roles in various abiotic stresses. Peanuts (Arachis hypogaea L.), one of the most important grain legumes and source of edible oils and proteins, are cultivated in the semi-arid tropical and subtropical regions of the world. To date, there has been no report on the role of miRNAs in the response to cold stress in cultivated peanuts. In this study, we profiled cold-responsive miRNAs in peanuts using deep sequencing in cold-sensitive (WQL20) alongside a tolerant variety (WQL30). A total of 407 known miRNAs and 143 novel peanut-specific miRNAs were identified. The expression of selected known and novel miRNAs was validated by northern blotting and six known cold-responsive miRNAs were revealed. Degradome sequencing identified six cold-responsive miRNAs that regulate 12 target genes. The correlative expression patterns of several miRNAs and their target genes were further validated using qRT-PCR. Our data showed that miR160-ARF, miR482-WDRL, miR2118-DR, miR396-GRF, miR162-DCL, miR1511-SRF, and miR1511-SPIRAL1 modules may mediate cold stress responses. Transient expression analysis in Nicotiana benthamiana found that miR160, miR482, and miR2118 may play positive roles, and miR396, miR162, and miR1511 play negative roles in the regulation of peanut cold tolerance. Our results provide a foundation for understanding miRNA-dependent cold stress response in peanuts. The characterized correlations between miRNAs and their response to cold stress could serve as markers in breeding programs or tools for improving cold tolerance of peanuts.

Genome-wide analysis of pathogenesis-related protein 1 (PR-1) gene family from Musa spp. and its role in defense response during stresses

Pathogenesis related protein-1 (PR-1) is the most abundantly produced protein during defense response against many biotic and abiotic stresses. However, knowledge on PR-1 gene family and its evolutionary relationship in banana is very limited. In order to study the potential role of PR-1 genes in banana, genome wide identification, structure analysis and expressions were performed. A total of 15 and 11 PR-1 genes were identified from A and B genomes of banana and the proteins encoded by this gene family are of varying lengths and harbor conserved domains and motifs. PR-1 genes are unevenly dispersed on 11 chromosomes with segmental duplication in both A and B genome, suggesting an important contribution of duplication in expansion of PR-1 gene family in banana. qRT-PCR analysis of PR-1 gene showed positive correlation with the RNAseq data under various stresses and examination of expression pattern of selected MaPR-1 genes in banana revealed its role in biotic and abiotic stresses in general and fusarium wilt in particular. This study provides significant insight into the functions of PR-1 genes which can be further exploited as a promising candidate for developing multiple stress tolerant banana varieties.

ARF6s Identification and Function Analysis Provide Insights Into Flower Development of Punica granatum L

Based on the genome and small-RNA sequencing of pomegranate, miRNA167 and three target genes PgARF6 were identified in "Taishanhong" genome. Three PgARF6 genes and their corresponding protein sequences, expression patterns in pomegranate flower development and under exogenous hormones treatments were systematically analyzed in this paper. We found that PgARF6s are nuclear proteins with conserved structures. However, PgARF6s had different protein structures and expression profiles in pomegranate flower development. At the critical stages of pomegranate ovule sterility (8.1-14.0 mm), the expression levels of PgARF6s in bisexual flowers were lower than those in functional male flowers. Interestingly, PgARF6c expression level was significantly higher than PgARF6a and PgARF6b. Under the treatment of exogenous IBA and 6-BA, PgARF6s were down-regulated, and the expression of PgARF6c was significantly inhibited. PgmiR167a and PgmiR167d had the binding site on PgARF6 genes sequences, and PgARF6a has the directly targeted regulatory relationship with PgmiR167a in pomegranate. At the critical stage of ovule development (8.1-12.0 mm), exogenous IBA and 6-BA promoted the content of GA and ZR accumulation, inhibited BR accumulation. There was a strong correlation between the expression of PgARF6a and PgARF6b. Under exogenous hormone treatment, the content of ZR, BR, GA, and ABA were negatively correlated with the expressions of PgARF6 genes. However, JA was positively correlated with PgARF6a and PgARF6c under IBA treatment. Thus, our results provide new evidence for PgARF6 genes involving in ovule sterility in pomegranate flowers.

Effect of the PmARF6 Gene from Masson Pine (Pinus massoniana) on the Development of Arabidopsis

Masson pine (Pinus massoniana) is a core industrial tree species that is used for afforestation in southern China. Previous studies have shown that Auxin Response Factors (ARFs) are involved in the growth and development of various species, but the function of ARFs in Masson pine is unclear. In this research, we cloned and identified Masson pine ARF6 cDNA (PmARF6). The results showed that PmARF6 encodes a protein of 681 amino acids that is highly expressed in female flowers. Subcellular analysis showed that the PmARF6 protein occurred predominantly in the nucleus and cytomembrane of Masson pine cells. Compared with wild-type (WT) Arabidopsis, transgenic Arabidopsis plants overexpressing PmARF6 had fewer rosette leaves, and their flower development was slower. These results suggest that overexpression of PmARF6 may inhibit the flower and leaf development of Masson pine and provide new insights into the underlying developmental mechanism.

F-box protein EBF1 and transcription factor ABI5-like regulate banana fruit chilling-induced ripening disorder

Cold stress adversely affects plant production, both qualitatively and quantitatively. Banana (Musa acuminata) is sensitive to cold stress and suffers chilling injury (CI) when stored under 11°C, causing abnormal fruit softening. However, the mechanism underlying the abnormal fruit softening due to CI remains obscure. This study uncovered the coordinated transcriptional mechanism of ethylene F-box (EBF1) protein and abscisic acid-insensitive 5 (ABI5)-like protein in regulating chilling-induced softening disorders of Fenjiao banana. Cold stress severely inhibited the transcript and protein levels of EBF1, ABI5-like, and fruit softening-related genes. The ABI5-like protein bound to the promoters of key starch and cell wall degradation-related genes such as β-amylase 8 (BAM8), pectate lyase 8 (PL8), and β-D-xylosidase23-like (XYL23-like) and activated their activities. EBF1 physically interacted with ABI5-like and enhanced the transcriptional activity of the key starch and cell wall degradation-related genes but did not ubiquitinate or degrade ABI5-like protein. This promoted fruit ripening and ameliorated fruit CI in a manner similar to the effect of exogenous abscisic acid treatment. The ectopic and transient overexpression of EBF1 and ABI5-like genes in tomato (Solanum lycopersicum) and Fenjiao banana accelerated fruit ripening and softening by promoting ethylene production, starch and cell wall degradation, and decreasing fruit firmness. EBF1 interacted with EIL4 but did not ubiquitinate or degrade EIL4, which is inconsistent with the typical role of EBF1/2 in Arabidopsis (Arabidopsis thaliana). These results collectively highlight that the interaction of EBF1 and ABI5-like controls starch and cell wall metabolism in banana, which is strongly inhibited by chilling stress, leading to fruit softening and ripening disorder.

The auxin response factor (ARF) gene family in Oil palm (Elaeis guineensis Jacq.): Genome-wide identification and their expression profiling under abiotic stresses

Auxin response factors (ARFs) play vital role in controlling growth and developmental processes of plants via regulating the auxin signaling pathways. However, the identification and functional roles of ARFs in oil palm plants remain elusive. Here, we identified a total of 23 ARF (EgARF) genes in oil palm through a genome-wide identification approach. The EgARF gene structure analysis revealed the presence of intron-rich ARF gene family in genome of oil palm. Further analysis demonstrated the uneven distribution of 23EgARFs on 16 chromosomes of oil palm. Phylogenetic analysis clustered all the EgARFs into four groups. Twenty-one EgARFs contained BDD, ARF, and CTD domains, whereas EgARF5 and EgARF7 lacked the CTD domain. The evolution of ARF genes in oil palm genome has been expanded by segmental duplication events. The cis-acting regulatory elements of EgARF gene family were predominantly associated with the stress and hormone responses. Expression profiling data demonstrated the constitutive and tissue-specific expression of EgARF genes in various tissues of oil palm. Real-time PCR analysis of 19 EgARF genes expression levels under cold, drought, and salt stress conditions proved their prominent role under abiotic stress responses. Altogether, our study provides a basis for studying the molecular and functional roles of ARF genes in oil palm.

OsCYP714D1 improves plant growth and salt tolerance through regulating gibberellin and ion homeostasis in transgenic poplar

Cytochrome P450 monooxygenases (CYP450s) play crucial roles in the regulation of plant growth and response to abiotic stress. However, their functions in woody trees are still largely unknown. Previously, we reported that expression of the rice cytochrome P450 monooxygenase gene OsCYP714D1 increased gibberellic acid (GA) accumulation and shoot growth in transgenic poplar. In this work, we demonstrate that expression of OsCYP714D1 improved the salt tolerance of transgenic poplar plants. Compared to wild type, plant height and K⁺ content were significantly higher, whereas plant growth inhibition and Na⁺ content were significantly lower, in transgenic plants grown under high salt stress condition. Transcriptomic analyses revealed that OsCYP714D1 expression up-regulated the expressions of GA biosynthesis, signaling and stress responsive genes in transgenic plants under both normal and high salt stress conditions. Further gene ontology (GO) analyses indicated that genes involved in plant hormone and ion metabolic activities were significantly enriched in transgenic plants. Our findings imply that OsCYP714D1 participated in the regulation of both shoot growth and salt resistance through regulating gibberellin and ion homeostasis in transgenic poplar, and it can be used as a candidate gene for the engineering of new tree varieties with improved biomass production and salt stress resistance.

A Novel Banana Mutant "RF 1" (Musa spp. ABB, Pisang Awak Subgroup) for Improved Agronomic Traits and Enhanced Cold Tolerance and Disease Resistance

Banana is a major fruit crop grown in tropical and subtropical regions worldwide. Among cultivars, "FenJiao, FJ" (Musa spp. ABB, Pisang Awak subgroup) is a popular variety of bananas, due to its better sugar-acid blend and relatively small fruit shape. However, because the traditional FJ variety grows relatively high in height, it is vulnerable to lodging and unsuitable for harvesting. In this study, we sought desirable banana mutants by carrying out ethyl methanesulfonate (EMS) mutagenesis with the FJ cultivar. After the FJ shoot tips had been treated with 0.8% (v/v) EMS for 4 h, we obtained a stably inherited mutant, here called "ReFen 1" (RF1), and also observed a semi-dwarfing phenotype. Compared with the wild type (FJ), this RF1 mutant featured consistently improved agronomic traits during 5-year field experiments conducted in three distinct locations in China. Notably, the RF1 plants showed significantly enhanced cold tolerance and Sigatoka disease resistance, mainly due to a substantially increased soluble content of sugar and greater starch accumulation along with reduced cellulose deposition. Therefore, this study not only demonstrated how a powerful genetic strategy can be used in fruit crop breeding but also provided insight into the identification of novel genes for agronomic trait improvement in bananas and beyond.

Genome-wide analysis of ARF transcription factors reveals HcARF5 expression profile associated with the biosynthesis of β-ocimene synthase in Hedychium coronarium

Herein, 37 ARF genes were identified and analyzed in Hedychium coronarium and HcARF5 showed a potential role in the regulation of HcTPS3. Auxin is an important plant hormone, implicated in various aspects of plant growth and development processes especially in the biosynthesis of various secondary metabolites. Auxin response factors (ARF) belong to the transcription factors (TFs) gene family and play a crucial role in transcriptional activation/repression of auxin-responsive genes by directly binding to their promoter region. Nevertheless, whether ARF genes are involved in the regulatory mechanism of volatile compounds in flowering plants is largely unknown. β-ocimene is a key floral volatile compound synthesized by terpene synthase 3 (HcTPS3) in Hedychium coronarium. A comprehensive analysis of H. coronarium genome reveals 37 candidate ARF genes in the whole genome. Tissue-specific expression patterns of HcARFs family members were assessed using available transcriptome data. Among them, HcARF5 showed a higher expression level in flowers, and significantly correlated with the key structural β-ocimene synthesis gene (HcTPS3). Furthermore, transcript levels of both genes were associated with the flower development. Under hormone treatments, the response of HcARF5 and HcTPS3, and the emission level of β-ocimene contents were evaluated. Subcellular and transcriptional activity assay showed that HcARF5 localizes to the nucleus and possesses transcriptional activity. Yeast one-hybrid (Y1H) and dual-luciferase assays revealed that HcARF5 directly regulates the transcriptional activity of HcTPS3. Yeast two-hybrid (Y2H) and bimolecular fluorescence complementation (BiFC) assays showed that HcARF5 interacts with scent-related HcIAA4, HcIAA6, and HcMYB1 in vivo. Overall, these results indicate that HcARF5 is potentially involved in the regulation of β-ocimene synthesis in H. coronarium.

Genome-wide analysis of ARF transcription factors reveals HcARF5 expression profile associated with the biosynthesis of β-ocimene synthase in Hedychium coronarium

Herein, 37 ARF genes were identified and analyzed in Hedychium coronarium and HcARF5 showed a potential role in the regulation of HcTPS3. Auxin is an important plant hormone, implicated in various aspects of plant growth and development processes especially in the biosynthesis of various secondary metabolites. Auxin response factors (ARF) belong to the transcription factors (TFs) gene family and play a crucial role in transcriptional activation/repression of auxin-responsive genes by directly binding to their promoter region. Nevertheless, whether ARF genes are involved in the regulatory mechanism of volatile compounds in flowering plants is largely unknown. β-ocimene is a key floral volatile compound synthesized by terpene synthase 3 (HcTPS3) in Hedychium coronarium. A comprehensive analysis of H. coronarium genome reveals 37 candidate ARF genes in the whole genome. Tissue-specific expression patterns of HcARFs family members were assessed using available transcriptome data. Among them, HcARF5 showed a higher expression level in flowers, and significantly correlated with the key structural β-ocimene synthesis gene (HcTPS3). Furthermore, transcript levels of both genes were associated with the flower development. Under hormone treatments, the response of HcARF5 and HcTPS3, and the emission level of β-ocimene contents were evaluated. Subcellular and transcriptional activity assay showed that HcARF5 localizes to the nucleus and possesses transcriptional activity. Yeast one-hybrid (Y1H) and dual-luciferase assays revealed that HcARF5 directly regulates the transcriptional activity of HcTPS3. Yeast two-hybrid (Y2H) and bimolecular fluorescence complementation (BiFC) assays showed that HcARF5 interacts with scent-related HcIAA4, HcIAA6, and HcMYB1 in vivo. Overall, these results indicate that HcARF5 is potentially involved in the regulation of β-ocimene synthesis in H. coronarium.

Genome-Wide Identification and Transcript Analysis of TCP Gene Family in Banana (Musa acuminata L.)

Plant-specific TEOSINTE-BRANCHED1/CYCLOIDEA/PROLIFERATING CELL FACTOR1 (TCP) gene family has versatile functions in diverse aspects of plants. However, less research on banana TCPs was done comprehensively. Accordingly, 48 banana TCP genes were characterized on aspects of gene structure, conserved motifs, phylogenetic relationship, and expression patterns. Members of the MaTCP gene family were unevenly distributed among 11 chromosomes and purification selection was the driving force of the MaTCP gene family. Gene duplication analysis indicated that segmental duplication is the major contributor to family expansion. Promoter analysis showed that MaTCPs might be involved in banana growth, development, and abiotic stress responses. Further, the expression of 12 MaTCPs was analyzed by real-time quantitative RT-PCR, and the protein interaction analysis showed that MaPCF10 and MaPCF13 may have an important function in banana fruit development and ripening. These results lay the foundation for further study of the functions of TCP genes in banana.

Genome-wide identification of AUX/IAA in radish and functional characterization of RsIAA33 gene during taproot thickening

Auxin/indole-3-acetic acid (Aux/IAA) genes encode short lived nuclear proteins that cooperated with auxin or auxin response factor (ARF), which are involved in plant growth and developmental processes. However, it's still ambiguous how the Aux/IAA genes regulate the process governing taproot thickening in radish. Herein, 65 Aux/IAA genes were identified from the radish genome. Gene duplication analysis showed that two pairs of tandem duplication and 17 (27%) segmental duplication events were identified among Aux/IAA family genes in radish. Transcriptomic analysis revealed that most of Aux/IAA genes (52/65) exhibited differential expression pattern in different root tissues, and six root-specific genes were highly expressed in root cortex, cambium, xylem, and root tip in radish. RT-qPCR analysis showed that the expression level of RsIAA33 was the highest at cortex splitting stage (CSS), and early expanding stage (ES). Furthermore, amiRNA-mediated gene silencing of RsIAA33 indicated that it could inhibit the reproductive growth, thus promoting taproot thickening and development. These results would provide valuable information for elucidating the molecular function of Aux/IAA genes involved in taproot thickening in radish.

Genome-wide identification of auxin response factor (ARF) family in kiwifruit (Actinidia chinensis) and analysis of their inducible involvements in abiotic stresses

Auxin response factor (ARF) acts as a vital component of auxin signaling and participates in growth, development, and stress responses in plants. In the present study, we comprehensively analyzed kiwifruit's (Actinidia chinensis) ARF genes (AcARFs) and their involvement in abiotic stress response. We identified a total of 41 AcARFs encoding ARFs in the A. chinensis genome. AcARF genes were characterized by the classic ARF_resp and a B3 domain and primarily localized on the cytoplasm and nucleus. AcARFs were categorized into eight subgroups as per the phylogenetic analysis. Synteny analysis showed that 35 gene pairs in AcARF family underwent segmental and whole genome duplication events. Promoter cis-element prediction revealed that AcARFs might be involved in abiotic factors related to stress response, which was later assessed and validated by qRT-PCR based expression analysis. Additionally, AcARFs showed tissue-specific expression. These findings extend our understanding of the functional roles of AcARFs in stress responses. Taken together, the systematic annotation of the AcARF family genes provides a platform for the functional and evolutionary study, which might help in elucidating the precise roles of the AcARFs in stress responses.

SUPPLEMENTARY INFORMATION

The online version contains supplementary material available at 10.1007/s12298-021-01011-4.

Crosstalk between phytohormones and secondary metabolites in the drought stress tolerance of crop plants: A review

Drought stress negatively affects crop performance and weakens global food security. It triggers the activation of downstream pathways, mainly through phytohormones homeostasis and their signaling networks, which further initiate the biosynthesis of secondary metabolites (SMs). Roots sense drought stress, the signal travels to the above-ground tissues to induce systemic phytohormones signaling. The systemic signals further trigger the biosynthesis of SMs and stomatal closure to prevent water loss. SMs primarily scavenge reactive oxygen species (ROS) to protect plants from lipid peroxidation and also perform additional defense-related functions. Moreover, drought-induced volatile SMs can alert the plant tissues to perform drought stress mitigating functions in plants. Other phytohormone-induced stress responses include cell wall and cuticle thickening, root and leaf morphology alteration, and anatomical changes of roots, stems, and leaves, which in turn minimize the oxidative stress, water loss, and other adverse effects of drought. Exogenous applications of phytohormones and genetic engineering of phytohormones signaling and biosynthesis pathways mitigate the drought stress effects. Direct modulation of the SMs biosynthetic pathway genes or indirect via phytohormones' regulation provides drought tolerance. Thus, phytohormones and SMs play key roles in plant development under the drought stress environment in crop plants.

Molecular and Hormonal Mechanisms Regulating Fleshy Fruit Ripening

This article focuses on the molecular and hormonal mechanisms underlying the control of fleshy fruit ripening and quality. Recent research on tomato shows that ethylene, acting through transcription factors, is responsible for the initiation of tomato ripening. Several other hormones, including abscisic acid (ABA), jasmonic acid (JA) and brassinosteroids (BR), promote ripening by upregulating ethylene biosynthesis genes in different fruits. Changes to histone marks and DNA methylation are associated with the activation of ripening genes and are necessary for ripening initiation. Light, detected by different photoreceptors and operating through ELONGATED HYPOCOTYL 5(HY5), also modulates ripening. Re-evaluation of the roles of 'master regulators' indicates that MADS-RIN, NAC-NOR, Nor-like1 and other MADS and NAC genes, together with ethylene, promote the full expression of genes required for further ethylene synthesis and change in colour, flavour, texture and progression of ripening. Several different types of non-coding RNAs are involved in regulating expression of ripening genes, but further clarification of their diverse mechanisms of action is required. We discuss a model that integrates the main hormonal and genetic regulatory interactions governing the ripening of tomato fruit and consider variations in ripening regulatory circuits that operate in other fruits.

Identification and expression of the BAHD family during development, ripening, and stress response in banana

The BAHD family is involved in different biological roles in plants, including secondary metabolite synthesis, improving abiotic/biotic stress resistance, and influencing fruit quality. However, the knowledge about BAHD in banana, an important fruit crop, is limited. In this study, 46 banana BAHD genes (MaBAHDs) were identified and divided into four groups according to phylogenetic analysis. Most of the MaBAHD genes in the same group presented similar conserved motifs and genetic structures. MaBAHD genes have similar expression patterns in two banana varieties, and more genes showed high expressions in the roots. The comprehensive MaBAHD gene expression patterns obtained from two varieties of banana showed valuable information regarding their participation in fruit development, ripening, and response to abiotic/biotic stresses, suggesting that they play key roles in these processes. The systematic analysis of MaBAHD genes offered basic insight for further gene functional assays and potential applications in genetically improving banana cultivars.

Transcriptome analysis provides molecular evidences for growth and adaptation of plant roots in cadimium-contaminated environments

Cadmium (Cd) is a detrimental element that can be toxic to plants. The physiological and biochemical responses of plants to Cd stress have been extensively studied, but the molecular mechanisms remain unclear. The present study showed that Cd severely inhibited the growth of roots and shoots and reduced plant biomass of mung bean seedlings. To further investigate the gene profiles and molecular processes in response Cd stress, transcriptome analyses of mung bean roots exposed to 100 μM Cd for 1, 5, and 9 days were performed. Cd treatment significantly decreased global gene expression levels at 5 and 9 d compared with the control. A total of 6737, 10279, and 9672 differentially expressed genes (DEGs) were identified in the 1-, 5-, and 9-day Cd-treated root tissues compared with the controls, respectively. Based on the analysis of DEG function annotation and enrichment, a pattern of mung bean roots response to Cd stress was proposed. The processes detoxification and antioxidative defense were involved in the early response of mung bean roots to Cd. Cd stress downregulated the expressions of a series of genes involved in cell wall biosynthesis, cell division, DNA replication and repair, and photosynthesis, while genes involved in signal transduction and regulation, transporters, secondary metabolisms, defense systems, and mitochondrial processes were upregulated in response to Cd, which might be contributed to the improvement of plant tolerance. Our results provide some novel insights into the molecular processes for growth and adaption of mung bean roots in response to Cd and many candidate genes for further biotechnological manipulations to improve plant tolerance to heavy metals.

Identification of Candidate Auxin Response Factors Involved in Pomegranate Seed Coat Development

Auxin response factors (ARFs) are transcription factors, regulating the auxin signaling pathways involved in plant development and related processes. In this study, we performed the genome-wide identification and characterization of ARFs in pomegranate and compared them with ARFs from three other species. Seventeen PgrARFs were identified and clustered into four groups, according to their phylogenetic relationship with the remaining 59 ARFs. A recent whole-genome duplication event in pomegranate may have contributed to the expansion and diversification of PgrARFs. Genomic truncation and variant splicing mechanisms contributed to the divergence of PgrARFs, a conclusion that was supported by different exon-intron structures of genes and incomplete conserved domains of PgrARFs in a specific phylogenetic group (group III). Interestingly, the absence of motifs from certain PgrARF genes corresponded to their low transcription levels, which contrasted to the highly expressed PgrARFs with intact motifs. Specifically, PgrARF1 and PgrARF2 highly expressed in both inner and outer seed coat, and phylogenetically related to Arabidopsis orthologs which mediates cell divisions in seed coat. We infer these two PgrARFs might involve in seed coat development through cell divisions in response to auxin regulation. These findings provided information on the characteristics and evolutionary relationships of PgrARFs, but also shed lights on their potential roles during seed coat development in pomegranate.

Auxin-mediated responses under salt stress: from developmental regulation to biotechnological applications

As sessile organisms, plants are exposed to multiple abiotic stresses commonly found in nature. To survive, plants have developed complex responses that involve genetic, epigenetic, cellular, and morphological modifications. Among different environmental cues, salt stress has emerged as a critical problem contributing to yield losses and marked reductions in crop production. Moreover, as the climate changes, it is expected that salt stress will have a significant impact on crop production in the agroindustry. On a mechanistic level, salt stress is known to be regulated by the crosstalk of many signaling molecules such as phytohormones, with auxin having been described as a key mediator of the process. Auxin plays an important role in plant developmental responses and stress, modulating a complex balance of biosynthesis, transport, and signaling that among other things, finely tune physiological changes in plant architecture and Na+ accumulation. In this review, we describe current knowledge on auxin's role in modulating the salt stress response. We also discuss recent and potential biotechnological approaches to tackling salt stress.

Genome-wide sequence identification and expression analysis of ARF family in sugar beet (Beta vulgaris L.) under salinity stresses

Auxin response factor (ARF) proteins respond to biological and abiotic stresses and play important roles in regulating plant growth and development. In this study, based on the genome-wide database of sugar beet, 16 BvARF proteins were identified. A detailed investigation into the BvARF family is performed, including analysis of the conserved domains, chromosomal locations, phylogeny, exon-intron structure, conserved motifs, subcellular localization, gene ontology (GO) annotations and expression profiles of BvARF under salt-tolerant condition. The majority of BvARF proteins contain B3 domain, AUX_RESP domain and AUX/IAA domain and a few lacked of AUX/IAA domain. Phylogenetic analysis suggests that the 16 BvARF proteins are clustered into six groups. Expression profile analysis shows that most of these BvARF genes in sugar beet under salinity stress were up-regulated or down-regulated to varying degrees and nine of the BvARF genes changed significantly. They were thought to have a significant response to salinity stress. The current study provides basic information for the BvARF genes and will pave the way for further studies on the roles of BvARF genes in regulating sugar beet's growth, development and responses to salinity stress.

ARF family identification in Tamarix chinensis reveals the salt responsive expression of TcARF6 targeted by miR167

Auxin response factors (ARFs) are important transcription factors (TFs) that are differentially expressed in response to various abiotic stresses. The important roles of ARFs and small RNA-ARF pathways in mediating plant growth and stress responses have emerged in several recent studies. However, no studies on the involvement of ARFs in tamarisk trees, which are resistant to salinity, have been conducted. In this study, systematic analysis revealed 12 TcARF genes belonging to five different groups in Tamarix chinensis. The microRNA response elements of miR160, which belongs to group I and miR167, which belongs to group III, were conserved in terms of their location and sequence. Moreover, digital gene expression profiles suggested that a potential miR167 target gene, TcARF6, was rapidly expressed in response to salt stress. Cloning of TcARF6 revealed that TcARF6 could be an activation TF with a glutamine-rich region and expression pattern analysis revealed that the expression of TcARF6 was significantly downregulated specifically in the roots. A significant negative correlation in the expression pattern of tch-miR167/TcARF6 indicated that this module may play a key role in the response to salt stress. Overall, these results provide basic information on the posttranscriptional regulation of TcARF6 for future investigations of the T. chinensis salt-stress response.

Down Regulation and Loss of Auxin Response Factor 4 Function Using CRISPR/Cas9 Alters Plant Growth, Stomatal Function and Improves Tomato Tolerance to Salinity and Osmotic Stress

Auxin controls multiple aspects of plant growth and development. However, its role in stress responses remains poorly understood. Auxin acts on the transcriptional regulation of target genes, mainly through Auxin Response Factors (ARF). This study focuses on the involvement of SlARF4 in tomato tolerance to salinity and osmotic stress. Using a reverse genetic approach, we found that the antisense down-regulation of SlARF4 promotes root development and density, increases soluble sugars content and maintains chlorophyll content at high levels under stress conditions. Furthermore, ARF4-as displayed higher tolerance to salt and osmotic stress through reduced stomatal conductance coupled with increased leaf relative water content and Abscisic acid (ABA) content under normal and stressful conditions. This increase in ABA content was correlated with the activation of ABA biosynthesis genes and the repression of ABA catabolism genes. Cu/ZnSOD and mdhar genes were up-regulated in ARF4-as plants which can result in a better tolerance to salt and osmotic stress. A CRISPR/Cas9 induced SlARF4 mutant showed similar growth and stomatal responses as ARF4-as plants, which suggest that arf4-cr can tolerate salt and osmotic stresses. Our data support the involvement of ARF4 as a key factor in tomato tolerance to salt and osmotic stresses and confirm the use of CRISPR technology as an efficient tool for functional reverse genetics studies.

Expression analysis of the BpARF genes in Betula platyphylla under drought stress

Auxin response factors (ARFs) play an important role in modulating plant growth and development processes by regulating the expression of auxin-responsive genes. However, the modes of action of ARFs in birch (Betula platyphylla) remain largely unknown. In this study, fifteen ARF genes were identified in the birch (B. platyphylla) genome. Bioinformatics analysis revealed that the 15 BpARF genes were unevenly distributed on 7 chromosomes. The 15 BpARF proteins clustered into 6 groups, and all of them contained ARF and B3 motifs. The cis-acting elements present within the promoters of the BpARF genes were mostly related to stress resistance. Expression analysis revealed that most of the BpARF genes were significantly upregulated or downregulated in response to drought treatment in at least one organ. In particular, the expression of BpARF1 was significantly induced by drought stress. The function of BpARF1 was further studied via a transient transformation system. Under drought stress conditions, compared with vector control plants, BpARF1 RNA interference (RNAi)-inhibited plants presented reduced reactive oxygen species (ROS) accumulation, enhanced peroxide (POD) and superoxide dismutase (SOD) activities, increased ascorbic acid (AsA) and proline contents, and reduced electrolyte leakage and water loss rates. Conversely, BpARF1 overexpression plants displayed the opposite physiological changes. These results suggest that the silencing of BpARF1 can improve the drought tolerance of B. platyphylla.

Genome-Wide Identification and Expression Analysis of Auxin Response Factor (ARF) Gene Family in Longan (Dimocarpus longan L.)

Auxin response factor (ARF) is the key regulator involved in plant development. Despite their physiological importance identified in various woody plants, the functions of ARF genes in longan were still not clear. In this study, 17 longan ARF genes (DlARF) were identified using the reference longan genome data. According to the phylogenetic relationships among longan, Arabidopsis and apple, DlARFs were divided into four classes. Most DlARFs showed a closer relationship with ARFs from apple than those from Arabidopsis. The analysis of gene structure and domain revealed high similarity of different ARF genes in the same class. Typical features of B3-type DNA binding domain (DBD) motif, Auxin Resp motifs, and a highly conserved C-terminal Phox and Bem1 (PB1) domain were present in all DlARFs except for DlARF-2,-3,-13 which lacked PBI domain. Expression profiles of 17 DlARF genes in longan different tissues showed that some DlARF genes were tissues-specific genes. Analysis of three longan transcriptomes showed seven DlARFs (DlARF-1,-2,-6,-8,-9,-11,-16) had higher expression levels during floral bud differentiation of common longan and in the buds of 'Sijimi', suggesting these genes may promote floral bud differentiation in longan. Further qPCR analysis showed that among seven DlARF genes, the expression levels of DlARF-2,-6,-11,-16 increased significantly during the physiological differentiation stage of longan floral buds, confirming that they may play a role in flowering induction. Promoter sequence analysis revealed cis-elements related to flowering induction such as low-temperature responsiveness motif and circadian control motif. Motifs linked with hormone response for instance Auxin, MeJA, Gibberellin, and Abscisic acid were also found in promoters. This study provides a comprehensive overview of the ARF gene family in longan. Our findings could provide new insights into the complexity of the regulation of ARFs at the transcription level that may be useful to develop breeding strategies to improve development or promote flowering in longan.

Comprehensive Atlas of Wheat (Triticum aestivum L.) AUXIN RESPONSE FACTOR Expression During Male Reproductive Development and Abiotic Stress

AUXIN RESPONSE FACTOR (ARF) proteins regulate a wide range of signaling pathways, from general plant growth to abiotic stress responses. Here, we performed a genome-wide survey in wheat (Triticum aestivum) and identified 69 TaARF members that formed 24 homoeologous groups. Phylogenetic analysis clustered TaARF genes into three clades, similar to ARF genes in Arabidopsis (Arabidopsis thaliana) and rice (Oryza sativa). Structural characterization suggested that ARF gene structure and domain composition are well conserved between plant species. Expression profiling revealed diverse patterns of TaARF transcript levels across a range of developmental stages, tissues, and abiotic stresses. A number of TaARF genes shared similar expression patterns and were preferentially expressed in anthers. Moreover, our systematic analysis identified three anther-specific TaARF genes (TaARF8, TaARF9, and TaARF21) whose expression was significantly altered by low temperature in thermosensitive genic male-sterile (TGMS) wheat; these TaARF genes are candidates to participate in the cold-induced male sterility pathway, and offer potential applications in TGMS wheat breeding and hybrid seed production. Moreover, we identified putative functions for a set of TaARFs involved in responses to abscisic acid and abiotic stress. Overall, this study characterized the wheat ARF gene family and generated several hypotheses for future investigation of ARF function during anther development and abiotic stress.

Auxin Response Factor 2A Is Part of the Regulatory Network Mediating Fruit Ripening Through Auxin-Ethylene Crosstalk in Durian

Fruit ripening is a highly coordinated developmental process driven by a complex hormonal network. Ethylene is the main regulator of climacteric fruit ripening. However, a putative role of other key phytohormones in this process cannot be excluded. We previously observed an increasing level of auxin during the post-harvest ripening of the durian fruit, which occurred concomitantly with the rise in the climacteric ethylene biosynthesis. Herein, we connect the key auxin signaling component, auxin response factors (ARFs), with the regulatory network that controls fruit ripening in durian through the identification and functional characterization of a candidate ripening-associated ARF. Our transcriptome-wide analysis identified 15 ARF members in durian (DzARFs), out of which 12 were expressed in the fruit pulp. Most of these DzARFs showed a differential expression, but DzARF2A had a marked ripening-associated expression pattern during post-harvest ripening in Monthong, a commercial durian cultivar from Thailand. Phylogenetic analysis of DzARF2A based on its tomato orthologue predicted a role in ripening through the regulation of ethylene biosynthesis. Transient expression of DzARF2A in Nicotiana benthamiana leaves significantly upregulated the expression levels of ethylene biosynthetic genes, pointing to a ripening-associated role of DzARF2A through the transcriptional regulation of ethylene biosynthesis. Dual-luciferase reporter assay determined that DzARF2A trans-activates durian ethylene biosynthetic genes. We previously reported significantly higher auxin level during post-harvest ripening in a fast-ripening cultivar (Chanee) compared to a slow-ripening one (Monthong). DzARF2A expression was significantly higher during post-harvest ripening in the fast-ripening cultivars (Chanee and Phuangmanee) compared to that of the slow-ripening ones (Monthong and Kanyao). Thus, higher auxin level could upregulate the expression of DzARF2A during ripening of a fast-ripening cultivar. The auxin-induced expression of DzARF2A confirmed its responsiveness to exogenous auxin treatment in a dose-dependent manner, suggesting an auxin-mediated role of DzARF2A in fruit ripening. We suggest that high DzARF2A expression would activate ARF2A-mediated transcription of ethylene biosynthetic genes, leading to increased climacteric ethylene biosynthesis (auxin-ethylene crosstalk) and faster ripening. Hence, we demonstrated DzARF2A as a new component of the regulatory network possibly mediating durian fruit ripening through transcriptional regulation of ethylene biosynthetic genes.

Identification and bioinformatic analysis of Aux/IAA family based on transcriptome data of Bletilla striata

Auxin/Indole-3-Acetic Acid (Aux/IAA) genes are involved in auxin signaling pathway and play an important role in plant growth and development. However, many studies focus on Aux/IAA gene families and much less known in Bletilla striata. In this study, a total of 27 Aux/IAA genes (BsIAA1-27) were cloned from the transcriptome of Bletilla striata. Based on a phylogenetic analysis of the Aux/IAA protein sequences from B. striata, Arabidopsis thaliana and Dendrobium officinale, the Aux/IAA genes of B. striata (BsIAAs) were categorized into 2 subfamilies and 9 groups. While BsIAAs were more closer to those of D. officinale compared to A. thaliana. EST-SSR marker mining test showed that 4 markers could be stably amplified with obvious polymorphisms among 4 landraces. Our results suggested that BsIAAs were involved in the process of tuber development and provided insights into functional roles of Aux/IAA genes in B. striata and other plants.

Identification and Characterization of Stress-Responsive TAS3-Derived TasiRNAs in Melon

Small interfering RNAs (siRNA) are key regulators of gene expression that play essential roles in diverse biological processes. Trans-acting siRNAs (tasiRNAs) are a class of plant-endogenous siRNAs that lead the cleavage of nonidentical transcripts. TasiRNAs are usually involved in fine-tuning development. However, increasing evidence supports that tasiRNAs may be involved in stress response. Melon is a crop of great economic importance extensively cultivated in semiarid regions frequently exposed to changing environmental conditions that limit its productivity. However, knowledge of the precise role of siRNAs in general, and of tasiRNAs in particular, in regulating the response to adverse environmental conditions is limited. Here, we provide the first comprehensive analysis of computationally inferred melon-tasiRNAs responsive to two biotic (viroid-infection) and abiotic (cold treatment) stress conditions. We identify two TAS3-loci encoding to length (TAS3-L) and short (TAS3-S) transcripts. The TAS candidates predicted from small RNA-sequencing data were characterized according to their chromosome localization and expression pattern in response to stress. The functional activity of cmTAS genes was validated by transcript quantification and degradome assays of the tasiRNA precursors and their predicted targets. Finally, the functionality of a representative cmTAS3-derived tasiRNA (TAS3-S) was confirmed by transient assays showing the cleavage of ARF target transcripts.

The Involvement of the Banana F-Box Protein MaEBF1 in Regulating Chilling-Inhibited Starch Degradation through Interaction with a MaNAC67-Like Protein

Low-temperature storage is a common strategy for preserving and transporting vegetables and fruits. However, many fruits are hypersensitive to chilling injury, including bananas. In the present study, storage conditions of 11 °C delayed the ripening of Fenjiao (Musa ABB Pisang Awak) banana, and the pulp could be softened after ethephon treatment. Storage conditions of 7 °C prevented fruit from fully softening, and fruit contained a significantly higher starch content and lower soluble sugar content. MaEBF1, a critical gene component in the ethylene signaling pathway, was repressed during ripening after fruit had been stored for 12 days at 7 °C. The expression of a series of starch degradation-related genes and a MaNAC67-like gene were also severely repressed. Both MaEBF1 and MaNAC67-like genes were ethylene-inducible and localized in the nucleus. MaNAC67-like protein was able to physically bind to the promoter of genes associated with starch degradation, including MaBAM6, MaSEX4, and MaMEX1. Yeast two-hybrid, GST-pull down, and BiFC assays showed that MaEBF1 interacted with the MaNAC67-like protein, and their interaction further activated the promoters of MaBAM6 and MaSEX4. The current study indicates that MaNAC67-like is a direct regulator of starch degradation and potential for involvement in regulating chilling-inhibited starch degradation by interacting with the ethylene signaling components in banana fruit. The present work paves the way for further functional analysis of MaEBF1 and MaNAC67-like in banana, which will be useful for understanding the regulation of banana starch metabolism and fruit ripening.

Sweet cherry fruit miRNAs and effect of high CO2 on the profile associated with ripening

157 known and 55 novel miRNAs were found in sweet cherry fruit. MiRNA target genes involved in fruit ripening and the differentially expressed miRNAs under CO₂ treatment were identified. MicroRNAs (miRNAs) are short non-coding RNAs and play important functions in many biological processes, including fruit ripening and senescence. In the current study, the high-throughput sequencing and bioinformatics methods were implemented to decipher the miRNAs landscape in sweet cherry fruit. A total of 157 known miRNAs belonging to 50 families and 55 putative novel miRNAs were found. Target genes of the miRNAs were predicted and genes involved in fruit ripening were found, including F-box proteins and TFs such as SPL, TCP, NAC, MYB, ARF and AP2/ERF. And these target genes were further confirmed by degradome sequencing. A regulatory network model was constructed to uncover the miRNAs and their targets involved in fruit ripening and senescence. Importantly, elevated carbon dioxide can significantly postpone the ripening and senescence of sweet cherry fruit and the differentially expressed miRNAs exposed to CO₂ were identified. These miRNAs included miR482j, miR6275, miR164, miR166, miR171, miR393, miR858, miR3627a, miR6284, miR6289 and miR7122b, and some of their functions were linked to fruit ripening. This study was the first report to profile miRNAs in sweet cherry fruit and it would provide more information for further study of miRNA roles in the ripening processes and their regulation mechanism underlying the effects of high carbon dioxide treatment on fruit ripening.

Identification, Expression, and Interaction Network Analyses of the CDPK Gene Family Reveal Their Involvement in the Development, Ripening, and Abiotic Stress Response in Banana

Calcium-dependent protein kinases (CDPKs) play vital roles in the regulation of plant growth, development, and tolerance to various abiotic stresses. However, little information is available for this gene family in banana. In this study, 44 CDPKs were identified in banana and were classified into four groups based on phylogenetic, gene structure, and conserved motif analyses. The majority of MaCDPKs generally exhibited similar expression patterns in the different tissues. Transcriptome analyses revealed that many CDPKs showed strong transcript accumulation at the early stages of fruit development and postharvest ripening in both varieties. Interaction network and co-expression analysis further identified some CDPKs-mediated network that was potentially active at the early stages of fruit development. Comparative expression analysis suggested that the high levels of CDPK expression in FJ might be related to its fast ripening characteristic. CDPK expression following the abiotic stress treatments indicated a significant transcriptional response to osmotic, cold, and salt treatment, as well as differential expression profiles, between BX and FJ. The findings of this study elucidate the transcriptional control of CDPKs in development, ripening, and the abiotic stress response in banana. Some tissue-specific, development/ripening-dependent, and abiotic stress-responsive candidate MaCDPK genes were identified for further genetic improvement of banana.

New insight into the molecular basis of cadmium stress responses of wild paper mulberry plant by transcriptome analysis

BACKGROUND

Heavy metal contamination is becoming a limitation to the utilization of soil and the distribution of vegetation. In particular, cadmium (Cd) pollution has had a serious impact on the food chain. Broussonetia papyrifera is a widely distributed pioneer tree species of heavy metal contaminated areas with important economic value. However, little is known about the genomic background of the Cd-tolerance mechanism in B. papyrifera.

RESULTS

The CdCl₂ responsive physiology was evaluated and proved to be involved in antioxidase activity and active oxygen species (ROS) accumulation. The leaf and root transcriptomes derived from B. papyrifera grown under normal and CdCl₂ stress conditions were systematically investigated using the Illumina HiSeq method. A total of 180,678,660 bp (27.1 GB) clean reads were assembled into 589,487 high-quality unigenes, of which 256,025 (43.43% of the total) and 250,251 (42.45% of the total) were aligned in Gene Ontology (GO) and Protein family (Pfam), respectively. A total of 24,414 differentially expressed genes (DEGs) were GO-annotated into 53, 23, 55, and 60 terms from the transcriptomes of root and leaf tissues under Cd stress and control conditions. A total of 117,547 Kyoto Encyclopedia of Genes and Genomes (KEGG) Orthology (KO)-annotated DEGs were enriched in at least 47 KEGG pathway terms among the four comparisons. Many genes encoding important transcription factors (e.g., auxin/indole-3-acetic acid (AUX/IAA), basic helix-loop-helix (bHLH), DNA-binding one zinc finger (Dof), and MYB) and proteins involved in plant-pathogen interactions, phenylpropanoid biosynthesis, plant hormone signal transduction, oxidative phosphorylation, carbon fixation, peroxisomes, flavonoid biosynthesis, and glutathione metabolism, among others, were substantially upregulated under CdCl₂ stress.

CONCLUSIONS

These genes represent important candidates for studying Cd-response mechanisms and molecular biology of B. papyrifera and related species. Our findings provide a genomic sequence resource for functional genetic assignments in B. papyrifera, which will help elucidate the molecular mechanisms of its Cd-stress responses and facilitate the bioremediation of heavy metal contaminated areas via breeding of new stress-tolerant cultivars.