Characterization of B-BOX gene family and their expression profiles under hormonal, abiotic and metal stresses in Poaceae plants

Identification of the BBX gene family in blueberry at different chromosome ploidy levels and fruit development and response under stress

BACKGROUND

Blueberry (Vaccinium spp.) fruits are rich in flavonoids such as anthocyanins and have a high nutritional value. The zinc finger protein transcription factor B-box (BBX) plays important roles in plant growth and development, hormone response, abiotic stress, and anthocyanin accumulation. However, studies on the BBX family in blueberry are lacking.

RESULTS

In total, 83 VcBBX and 24 VdBBX genes were identified in tetraploid and diploid blueberry, respectively. A correlation was observed between the number of BBX genes in blueberry and chromosome ploidy. Gene loss and specific replication during blueberry evolution may lead to an imbalance of quantitative relationship between VcBBX and VdBBX genes. The analysis of transcriptome and quantitative reverse transcription-polymerase chain reaction data revealed that the expression pattern of BBX genes depended on the developmental stage of blueberry fruit. Gibberellin inhibited the expression of most VcBBX genes. Abscisic acid promoted the expression of some members of the BBX family. The expression levels of VcBBX15b4, VcBBX21a1, and VcBBX30a in blueberry leaves were significantly downregulated under blue light treatment, whereas that of VcBBX15c3 was significantly upregulated under red light treatment.

CONCLUSION

In total, 83 VcBBX and 24 VdBBX genes were identified in 2 types of blueberries. Fruit development and transcription profiles under different stresses were analyzed. These findings will support further investigation of how BBX genes are involved in regulating hormone treatment and light stress during the growth and development of blueberry.

The B-box transcription factor BnBBX22.A07 enhances salt stress tolerance by indirectly activating BnWRKY33.C03

Salt stress has a detrimental impact on both plant growth and global crop yields. B-box proteins have emerged as pivotal players in plant growth and development regulation. Although the precise role of B-box proteins orchestrating salt stress responses in B. napus (Brassica napus) is not well understood in the current literature, further research and molecular explorations are required. Here, we isolated the B-box protein BnBBX22.A07 from B. napus. The overexpression of BnBBX22.A07 significantly improved the salt tolerance of Arabidopsis (Arabidopsis thaliana) and B. napus. Transcriptomic and histological analysis showed that BnBBX22.A07 enhanced the salt tolerance of B. napus by activating the expression of reactive oxygen species (ROS) scavenging-related genes and decreasing salt-induced superoxide anions and hydrogen peroxide. Moreover, BnBBX22.A07 interacted with BnHY5.C09, which specifically bound to and activated the promoter of BnWRKY33.C03. The presence of BnBBX22.A07 enhanced the activation of BnHY5.C09 on BnWRKY33.C03. Overexpression of BnHY5.C09 and BnWRKY33.C03 improved the salt tolerance of Arabidopsis. Functional analyses revealed that BnBBX22.A07-mediated salt tolerance was partly dependent on WRKY33. Taken together, we demonstrate that BnBBX22.A07 functions positively in salt responses not only by activating ROS scavenging-related genes but also by indirectly activating BnWRKY33.C03. Notably, our study offers a promising avenue for the identification of candidate genes that could be harnessed in breeding endeavours to develop salt-resistant transgenic crops.

Data-driven identification of environmental variables influencing phenotypic plasticity to facilitate breeding for future climates

Phenotypic plasticity describes a genotype's ability to produce different phenotypes in response to different environments. Breeding crops that exhibit appropriate levels of plasticity for future climates will be crucial to meeting global demand, but knowledge of the critical environmental factors is limited to a handful of well-studied major crops. Using 727 maize (Zea mays L.) hybrids phenotyped for grain yield in 45 environments, we investigated the ability of a genetic algorithm and two other methods to identify environmental determinants of grain yield from a large set of candidate environmental variables constructed using minimal assumptions. The genetic algorithm identified pre- and postanthesis maximum temperature, mid-season solar radiation, and whole season net evapotranspiration as the four most important variables from a candidate set of 9150. Importantly, these four variables are supported by previous literature. After calculating reaction norms for each environmental variable, candidate genes were identified and gene annotations investigated to demonstrate how this method can generate insights into phenotypic plasticity. The genetic algorithm successfully identified known environmental determinants of hybrid maize grain yield. This demonstrates that the methodology could be applied to other less well-studied phenotypes and crops to improve understanding of phenotypic plasticity and facilitate breeding crops for future climates.

A tomato B-box protein regulates plant development and fruit quality through the interaction with PIF4, HY5, and RIN transcription factors

During the last decade, knowledge about BBX proteins has greatly increased. Genome-wide studies identified the BBX gene family in several ornamental, industry, and food crops; however, reports regarding the role of these genes as regulators of agronomically important traits are scarce. Here, by phenotyping a knockout mutant, we performed a comprehensive functional characterization of the tomato locus Solyc12g089240, hereafter called SlBBX20. The data revealed the encoded protein as a positive regulator of light signaling affecting several physiological processes during the life span of plants. Through inhibition of PHYTOCHROME INTERACTING FACTOR 4 (SlPIF4)-auxin crosstalk, SlBBX20 regulates photomorphogenesis. Later in development, it controls the balance between cell division and expansion to guarantee correct vegetative and reproductive development. In fruits, SlBBX20 is transcriptionally induced by the master transcription factor RIPENING INHIBITOR (SlRIN) and, together with ELONGATED HYPOCOTYL 5 (SlHY5), up-regulates flavonoid biosynthetic genes. Finally, SlBBX20 promotes the accumulation of steroidal glycoalkaloids and attenuates Botrytis cinerea infection. This work clearly demonstrates that BBX proteins are multilayer regulators of plant physiology because they affect not only multiple processes during plant development but they also regulate other genes at the transcriptional and post-translational levels.

Dual-Model GWAS Analysis and Genomic Selection of Maize Flowering Time-Related Traits

An appropriate flowering period is an important selection criterion in maize breeding. It plays a crucial role in the ecological adaptability of maize varieties. To explore the genetic basis of flowering time, GWAS and GS analyses were conducted using an associating panel consisting of 379 multi-parent DH lines. The DH population was phenotyped for days to tasseling (DTT), days to pollen-shedding (DTP), and days to silking (DTS) in different environments. The heritability was 82.75%, 86.09%, and 85.26% for DTT, DTP, and DTS, respectively. The GWAS analysis with the FarmCPU model identified 10 single-nucleotide polymorphisms (SNPs) distributed on chromosomes 3, 8, 9, and 10 that were significantly associated with flowering time-related traits. The GWAS analysis with the BLINK model identified seven SNPs distributed on chromosomes 1, 3, 8, 9, and 10 that were significantly associated with flowering time-related traits. Three SNPs 3_198946071, 9_146646966, and 9_152140631 showed a pleiotropic effect, indicating a significant genetic correlation between DTT, DTP, and DTS. A total of 24 candidate genes were detected. A relatively high prediction accuracy was achieved with 100 significantly associated SNPs detected from GWAS, and the optimal training population size was 70%. This study provides a better understanding of the genetic architecture of flowering time-related traits and provides an optimal strategy for GS.

Genome-Wide Identification of Peanut B-Boxs and Functional Characterization of AhBBX6 in Salt and Drought Stresses

The B-box (BBX) gene family includes zinc finger protein transcription factors that regulate a multitude of physiological and developmental processes in plants. While BBX gene families have been previously determined in various plants, the members and roles of peanut BBXs are largely unknown. In this research, on the basis of the genome-wide identification of BBXs in three peanut species (Arachis hypogaea, A. duranensis, and A. ipaensis), we investigated the expression profile of the BBXs in various tissues and in response to salt and drought stresses and selected AhBBX6 for functional characterization. We identified a total of 77 BBXs in peanuts, which could be grouped into five subfamilies, with the genes from the same branch of the same subgroup having comparable exon-intron structures. In addition, a significant number of cis-regulatory elements involved in the regulation of responses to light and hormones and abiotic stresses were found in the promoter region of peanut BBXs. Based on the analysis of transcriptome data and qRT-PCR, we identified AhBBX6, AhBBX11, AhBBX13, and AhBBX38 as potential genes associated with tolerance to salt and drought. Silencing AhBBX6 using virus-induced gene silencing compromised the tolerance of peanut plants to salt and drought stresses. The results of this study provide knowledge on peanut BBXs and establish a foundation for future research into their functional roles in peanut development and stress response.

A B-box transcription factor OsBBX17 regulates saline-alkaline tolerance through the MAPK cascade pathway in rice

Rice OsBBX17 encodes a B-box zinc finger transcription factor in which the N-terminal B-box structural domain interacts with OsMPK1. In addition, it directly binds to the G-box of OsHAK2 and OsHAK7 promoters and represses their transcription. Under saline-alkaline conditions, the expression of OsBBX17 was inhibited. Meanwhile, activation of the OsMPK1-mediated mitogen-activated protein kinase cascade pathway caused OsMPK1 to interact with OsBBX17 and phosphorylate OsBBX17 at the Thr-95 site. It reduced OsBBX17 DNA-binding activity and enhanced saline-alkaline tolerance by deregulating transcriptional repression of OsHAK2 and OsHAK7. Genetic assays showed that the osbbx17-KO had an excellent saline-alkaline tolerance, whereas the opposite was in OsBBX17-OE. In addition, overexpression of OsMPK1 significantly improved saline-alkaline tolerance, but knockout of OsMPK1 caused an increased sensitivity. Further overexpression of OsBBX17 in the osmpk1-KO caused extreme saline-alkaline sensitivity, even a quick death. OsBBX17 was validated in saline-alkaline tolerance from two independent aspects, transcriptional level and post-translational protein modification, unveiling a mechanistic framework by which OsMPK1-mediated phosphorylation of OsBBX17 regulates the transcription of OsHAK2 and OsHAK7 to enhance the Na+ /K+ homeostasis, which partially explains light on the molecular mechanisms of rice responds to saline-alkaline stress via B-box transcription factors for the genetic engineering of saline-alkaline tolerant crops.

Assessment of physio-biochemical assessment and gene expression analysis of sugarcane genotypes under water stress

BACKGROUND

Sugarcane, an economically important crop cultivated for its unique character of accumulating sucrose into its stalk and the world's major crop according to production quantity. Sugarcane production is negatively influenced by abiotic stresses because it faces all types of environments due to its long-life cycle period. Among the various abiotic stresses, drought is one of the major limiting factors creates obstacle in sugarcane production. Thus, an attempt was made to assess the molecular insights into sugarcane genotypes under water stress. A preliminary screening was done in ten sugarcane genotypes grown under semi-arid region of India through physiological, biochemical and antioxidant responses of these genotypes under two water deficit levels.

METHODS

In the current study, drought was imposed on ten sugarcane genotypes during their formative stage (110 DAP) by depriving them of irrigation. A pot experiment was carried out to see how several commercial sugarcane genotypes responded to water scarcity. Sugarcane received two treatments, the first after 125 days and the second after 140 days. The physio-biochemical and antioxidant responses recorded were RWC, MSI, SCMR, Proline accumulation, SOD, Catalase, Peroxidase and Lipid peroxidation. The significant variations were recorded in responses of all genotypes. On the basis of physio-biochemical, three genotypes Cos 98,014, Cos 13,235 and Colk 14,201 were selected for differential gene expression pattern analysis. The total RNA was isolated and reverse transcribe to cDNA and real time PCR was performed for expression analysis under 10 genes.

RESULTS

Under drought conditions, all sugarcane genotypes showed significantly decreased RWC, chlorophyll content, and MSI. However, when water was scarce, proline buildup, malondialdehyde (MDA) contents, enzymatic antioxidant activity (CAT, POD, and SOD), and contents all increased dramatically. Finally, in all physiological and biochemical parameters, Co 98,014 genotype displayed superior adaptation responses to drought stress, followed by Co 018, Cos 13,235, and Colk 14,201. For gene expression analysis out of 21 genes, 10 genes were expressed in sugarcane genotypes, in which 7 genes (Shbbx2, Shbbx3, Shbbx4, Shbbx5, Shbbx8, Shbbx15 and Shbbx20) were upregulated and 3 genes (Shbbx1, Shbbx16 and Shbbx17) were downregulated.

CONCLUSION

The statistical analysis conducted in this study demonstrated that drought stress had a negative impact on physiological responses, including RWC, SPAD, and MSI, in sugarcane crops. However, it was found that the crops were able to survive in these stress conditions by increasing their biochemical parameters, all while maintaining their growth and function.

Genome-Wide Identification, Expression, and Molecular Characterization of the CONSTANS-like Gene Family in Seven Orchid Species

The orchid is one of the most distinctive and highly valued flowering plants. Nevertheless, the CONSTANS-like (COL) gene family plays significant roles in the control of flowering, and its functions in Orchidaceae have been minimally explored. This research identified 68 potential COL genes within seven orchids' complete genome, divided into three groups (groups I, II, and III) via a phylogenetic tree. The modeled three-dimensional structure and the conserved domains exhibited a high degree of similarity among the orchid COL proteins. The selection pressure analysis showed that all orchid COLs suffered a strong purifying selection. Furthermore, the orchid COL genes exhibited functional and structural heterogeneity in terms of collinearity, gene structure, cis-acting elements within their promoters, and expression patterns. Moreover, we identified 50 genes in orchids with a homology to those involved in the COL transcriptional regulatory network in Arabidopsis. Additionally, the first overexpression of CsiCOL05 and CsiCOL09 in Cymbidium sinense protoplasts suggests that they may antagonize the regulation of flowering time and gynostemium development. Our study will undoubtedly provide new resources, ideas, and values for the modern breeding of orchids and other plants.

SlMPK1- and SlMPK2-mediated SlBBX17 phosphorylation positively regulates CBF-dependent cold tolerance in tomato

B-box (BBX) proteins are an important class of zinc finger transcription factors that play a critical role in plant growth and stress response. However, the mechanisms of how BBX proteins participate in the cold response in tomato remain unclear. Here, using approaches of reverse genetics, biochemical and molecular biology we characterized a BBX transcription factor, SlBBX17, which positively regulates cold tolerance in tomato (Solanum lycopersicum). Overexpressing SlBBX17 enhanced C-repeat binding factor (CBF)-dependent cold tolerance in tomato plants, whereas silencing SlBBX17 increased plant susceptibility to cold stress. Crucially, the positive role of SlBBX17 in CBF-dependent cold tolerance was dependent on ELONGATED HYPOCOTYL5 (HY5). SlBBX17 physically interacted with SlHY5 to directly promote the protein stability of SlHY5 and subsequently increased the transcriptional activity of SlHY5 on SlCBF genes under cold stress. Further experiments showed that cold-activated mitogen-activated protein kinases, SlMPK1 and SlMPK2, also physically interact with and phosphorylate SlBBX17 to enhance the interaction between SlBBX17 and SlHY5, leading to enhanced CBF-dependent cold tolerance. Collectively, the study unveiled a mechanistic framework by which SlMPK1/2-SlBBX17-SlHY5 regulated transcription of SlCBFs to enhance cold tolerance, thereby shedding light on the molecular mechanisms of how plants respond to cold stress via multiple transcription factors.

Identification and Characterization of the BBX Gene Family in Bambusa pervariabilis × Dendrocalamopsis grandis and Their Potential Role under Adverse Environmental Stresses

Zinc finger protein (ZFP) transcription factors play a pivotal role in regulating plant growth, development, and response to biotic and abiotic stresses. Although extensively characterized in model organisms, these genes have yet to be reported in bamboo plants, and their expression information is lacking. Therefore, we identified 21 B-box (BBX) genes from a transcriptome analysis of Bambusa pervariabilis × Dendrocalamopsis grandis. Consequently, multiple sequence alignments and an analysis of conserved motifs showed that they all had highly similar structures. The BBX genes were divided into four subgroups according to their phylogenetic relationships and conserved domains. A GO analysis predicted multiple functions of the BBX genes in photomorphogenesis, metabolic processes, and biological regulation. We assessed the expression profiles of 21 BBX genes via qRT-PCR under different adversity conditions. Among them, eight genes were significantly up-regulated under water deficit stress (BBX4, BBX10, BBX11, BBX14, BBX15, BBX16, BBX17, and BBX21), nine under salt stress (BBX2, BBX3, BBX7, BBX9, BBX10, BBX12, BBX15, BBX16, and BBX21), twelve under cold stress (BBX1, BBX2, BBX4, BBX7, BBX10, BBX12, BBX14, BBX15, BBX17, BBX18, BBX19, and BBX21), and twelve under pathogen infestation stress (BBX1, BBX2, BBX4, BBX7, BBX10, BBX12, BBX14, BBX15, BBX17, BBX18, BBX19, and BBX21). Three genes (BBX10, BBX15, and BBX21) were significantly up-regulated under both biotic and abiotic stresses. These results suggest that the BBX gene family is integral to plant growth, development, and response to multivariate stresses. In conclusion, we have comprehensively analyzed the BDBBX genes under various adversity stress conditions, thus providing valuable information for further functional studies of this gene family.

Comprehensive Characterization of B-Box Zinc Finger Genes in Citrullus lanatus and Their Response to Hormone and Abiotic Stresses

Plant B-BOX (BBX) zinc finger transcription factors play crucial roles in growth and development and the stress response. Although the BBX family has been characterized in various plants, systematic analysis in watermelon is still lacking. In this study, 25 watermelon ClBBX genes were identified. ClBBXs were grouped into five clades (Clade I, II, III, IV, and V) based on their conserved domains and phylogenetic relationships. Most of the ClBBXs (84%) might be localized in the nuclei or cytoplasm. The classification of ClBBXs was consistent with their gene structures. They were unevenly distributed in nine chromosomes except for Chr4 and Chr10, with the largest number of six members in Chr2. Segmental duplications were the major factor in ClBBX family expansion. Some BBXs of watermelon and Arabidopsis evolved from a common ancestor. In total, 254 hormonal and stress-responsive cis elements were discovered in ClBBX promoters. ClBBXs were differentially expressed in tissues, and the expression levels of ClBBX15 and 16 were higher in aboveground tissues than in roots, while the patterns of ClBBX21a, 21b, 21c, 28 and 30b were the opposite. With salicylic acid, methyl jasmonate and salt stress conditions, 17, 18 and 18 ClBBXs exhibited significant expression changes, respectively. In addition, many ClBBXs, including ClBBX29b, 30a and 30b, were also responsive to cold and osmotic stress. In summary, the simultaneous response of multiple ClBBXs to hormonal or abiotic stress suggests that they may have functional interactions in the stress hormone network. Clarifying the roles of key ClBBXs in transcriptional regulation and mediating protein interactions will be an important task. Our comprehensive characterization of the watermelon ClBBX family provides vital clues for the in-depth analysis of their biological functions in stress and hormone signaling pathways.

OsBBX19-OsBTB97/OsBBX11 module regulates spikelet development and yield production in rice

Spikelet and floral-related organs are important agronomic traits for rice grain yield. BTB (broad-complex, tram track, and bric-abrac) proteins control various developmental functions in plants; however, the molecular mechanism of BTB proteins underlying grain development and yield production is still unknown. Here, we evaluated the molecular mechanism of a previously unrecognized functional gene, namely OsBTB97 that regulates the floral and spikelet-related organs which greatly affect the final grain yield. We found that the knockdown of the OsBTB97 gene had significant impacts on the development of spikelet-related organs and grain size, resulting in a decrease in yield, by altering the transcript levels of various spikelet- and grain-related genes. Furthermore, we found that the knockout mutants of two BBX genes, OsBBX11 and OsBBX19, which interact with the OsBTB97 protein at translation and transcriptional level, respectively, displayed lower OsBTB97 expression, suggesting the genetic relationship between the BTB protein and the BBX transcription factors in rice. Taken together, our study dissects the function of the novel OsBTB97 by interacting with two BBX proteins and an OsBBX19-OsBTB97/OsBBX11 module might function in the spikelet development and seed production in rice. The outcome of the present study provides promising knowledge about BTB proteins in the improvement of crop production in plants.

Genome-Wide Identification of B-Box Gene Family and Expression Analysis Suggest Its Roles in Responses to Cercospora Leaf Spot in Sugar Beet (Beta Vulgaris L.)

The B-box (BBX) protein, which is a zinc-finger protein containing one or two B-box domains, plays a crucial role in the growth and development of plants. Plant B-box genes are generally involved in morphogenesis, the growth of floral organs, and various life activities in response to stress. In this study, the sugar beet B-box genes (hereafter referred to as BvBBXs) were identified by searching the homologous sequences of the Arabidopsis thaliana B-box gene family. The gene structure, protein physicochemical properties, and phylogenetic analysis of these genes were systematically analyzed. In this study, 17 B-box gene family members were identified from the sugar beet genome. A B-box domain can be found in all sugar beet BBX proteins. BvBBXs encode 135 to 517 amino acids with a theoretical isoelectric point of 4.12 to 6.70. Chromosome localization studies revealed that BvBBXs were dispersed across nine sugar beet chromosomes except chromosomes 5 and 7. The sugar beet BBX gene family was divided into five subfamilies using phylogenetic analysis. The gene architectures of subfamily members on the same evolutionary tree branch are quite similar. Light, hormonal, and stress-related cis-acting elements can be found in the promoter region of BvBBXs. The BvBBX gene family was differently expressed in sugar beet following Cercospora leaf spot infection, according to RT-qPCR data. It is shown that the BvBBX gene family may influence how the plant reacts to a pathogen infection.

Characterization of Malectin/Malectin-like Receptor-like Kinase Family Members in Foxtail Millet (Setaria italica L.)

Plant malectin/malectin-like receptor-like kinases (MRLKs) play crucial roles throughout the life course of plants. Here, we identified 23 SiMRLK genes from foxtail millet. All the SiMRLK genes were named according to the chromosomal distribution of the SiMRLKs in the foxtail millet genome and grouped into five subfamilies based on phylogenetic relationships and structural features. Synteny analysis indicated that gene duplication events may take part in the evolution of SiMRLK genes in foxtail millet. The expression profiles of 23 SiMRLK genes under abiotic stresses and hormonal applications were evaluated through qRT-PCR. The expression of SiMRLK1, SiMRLK3, SiMRLK7 and SiMRLK19 were significantly affected by drought, salt and cold stresses. Exogenous ABA, SA, GA and MeJA also obviously changed the transcription levels of SiMRLK1, SiMRLK3, SiMRLK7 and SiMRLK19. These results signified that the transcriptional patterns of SiMRLKs showed diversity and complexity in response to abiotic stresses and hormonal applications in foxtail millet.

Biocuration of a Transcription Factors Network Involved in Submergence Tolerance during Seed Germination and Coleoptile Elongation in Rice (Oryza sativa)

Modeling biological processes and genetic-regulatory networks using in silico approaches provides a valuable framework for understanding how genes and associated allelic and genotypic differences result in specific traits. Submergence tolerance is a significant agronomic trait in rice; however, the gene-gene interactions linked with this polygenic trait remain largely unknown. In this study, we constructed a network of 57 transcription factors involved in seed germination and coleoptile elongation under submergence. The gene-gene interactions were based on the co-expression profiles of genes and the presence of transcription factor binding sites in the promoter region of target genes. We also incorporated published experimental evidence, wherever available, to support gene-gene, gene-protein, and protein-protein interactions. The co-expression data were obtained by re-analyzing publicly available transcriptome data from rice. Notably, this network includes OSH1, OSH15, OSH71, Sub1B, ERFs, WRKYs, NACs, ZFP36, TCPs, etc., which play key regulatory roles in seed germination, coleoptile elongation and submergence response, and mediate gravitropic signaling by regulating OsLAZY1 and/or IL2. The network of transcription factors was manually biocurated and submitted to the Plant Reactome Knowledgebase to make it publicly accessible. We expect this work will facilitate the re-analysis/re-use of OMICs data and aid genomics research to accelerate crop improvement.

OsMBTB32, a MATH-BTB domain-containing protein that interacts with OsCUL1s to regulate salt tolerance in rice

MATH-BTB proteins are involved in a variety of cellular processes that regulate cell homeostasis and developmental processes. Previous studies reported the involvement of BTB proteins in the development of various organs in plants; however, the function of BTB proteins in salt stress is less studied. Here, we found a novel MATH-BTB domain-containing OsMBTB32 protein that was highly expressed in leaf, root, and shoot. The up-regulation of the OsMBTB32 transcript in 2-week-old seedlings under salt stress suggests the significant role of the OsMBTB32 gene in salinity. The OsMBTB32 transgenic seedlings (OE and RNAi) exhibited significant differences in various phenotypes, including plumule, radical, primary root, and shoot length, compared to WT seedlings. We further found that OsCUL1 proteins, particularly OsCUL1-1 and OsCUL1-3, interact with OsMBTB32 and may suppress the function of OsMBTB32 during salt stress. Moreover, OsWRKY42, a homolog of ZmWRKY114 which negatively regulates salt stress in rice, directly binds to the W-box of OsCUL1-1 and OsCUL1-3 promoters to promote the interaction of OsCUL1-1 and OsCUL1-3 with OsMBTB32 protein in rice. The overexpression of OsMBTB32 and OsCUL1-3 further confirmed the function of OsMBTB32 and OsCUL1s in salt tolerance in Arabidopsis. Overall, the findings of the present study provide promising knowledge regarding the MATH-BTB domain-containing proteins and their role in enhancing the growth and development of rice under salt stress.MATH-BTB proteins are involved in a variety of cellular processes that regulate cell homeostasis and developmental processes. Previous studies reported the involvement of BTB proteins in the development of various organs in plants; however, the function of BTB proteins in salt stress is less studied. Here, we found a novel MATH-BTB domain-containing OsMBTB32 protein that was highly expressed in leaf, root, and shoot. The up-regulation of the OsMBTB32 transcript in 2-week-old seedlings under salt stress suggests the significant role of the OsMBTB32 gene in salinity. The OsMBTB32 transgenic seedlings (OE and RNAi) exhibited significant differences in various phenotypes, including plumule, radical, primary root, and shoot length, compared to WT seedlings. We further found that OsCUL1 proteins, particularly OsCUL1-1 and OsCUL1-3, interact with OsMBTB32 and may suppress the function of OsMBTB32 during salt stress. Moreover, OsWRKY42, a homolog of ZmWRKY114 which negatively regulates salt stress in rice, directly binds to the W-box of OsCUL1-1 and OsCUL1-3 promoters to promote the interaction of OsCUL1-1 and OsCUL1-3 with OsMBTB32 protein in rice. The overexpression of OsMBTB32 and OsCUL1-3 further confirmed the function of OsMBTB32 and OsCUL1s in salt tolerance in Arabidopsis. Overall, the findings of the present study provide promising knowledge regarding the MATH-BTB domain-containing proteins and their role in enhancing the growth and development of rice under salt stress.

Characterization of the B-BOX gene family in pepper and the role of CaBBX14 in defense response against Phytophthora capsici infection

The B-box (BBX) transcription factors are widely implicated in plant growth, development, and response to various biotic and abiotic stresses. However, their roles in the response of pepper to Phytophthora capsici infection (PCI) remain largely unexplored. Here, we report a total of 25 CaBBX genes with an uneven distribution were identified in pepper genome, and their characteristics, phylogenetic relationships, gene structures, conserved domains, and expression profiles were validated. CaBBXs were classified into five major clades (I to V) based on their phylogenetic relationships and conserved domains (presence of one or two B-box domains and a CCT domain). Gene duplication analysis demonstrated that there are two segmental duplication events but no tandem duplication event within pepper genome. Conserved motif and gene structure analysis revealed that the CaBBXs in the same clade have relatively similar motif arrangements and exon-intron patterns. Expression analysis revealed that the CaBBX genes have different expression levels in various tissues, and some of which were significantly induced during PCI and exogenous salicylic acid (SA) treatment. Among them, CaBBX14 displayed remarkable changed expression during PCI and SA treatment. The silencing of CaBBX14 increases pepper susceptibility to PCI, and also decreases in SA content and expression of pathogenesis-related (PR) and SA-related genes compared with control plants. Together, these findings advance our knowledge base on biological functions of CaBBXs in pepper during PCI through the SA signaling pathway, and we provide an example demonstrating that the potential of CaBBX14 to improve pepper resistance to PCI.

Responses of sorghum to cold stress: A review focused on molecular breeding

Climate change has led to the search for strategies to acclimatize plants to various abiotic stressors to ensure the production and quality of crops of commercial interest. Sorghum is the fifth most important cereal crop, providing several uses including human food, animal feed, bioenergy, or industrial applications. The crop has an excellent adaptation potential to different types of abiotic stresses, such as drought, high salinity, and high temperatures. However, it is susceptible to low temperatures compared with other monocotyledonous species. Here, we have reviewed and discussed some of the research results and advances that focused on the physiological, metabolic, and molecular mechanisms that determine sorghum cold tolerance to improve our understanding of the nature of such trait. Questions and opportunities for a comprehensive approach to clarify sorghum cold tolerance or susceptibility are also discussed.

Characterization and expression profiles of the B-box gene family during plant growth and under low-nitrogen stress in Saccharum

BACKGROUND

B-box (BBX) zinc-finger transcription factors play crucial roles in plant growth, development, and abiotic stress responses. Nevertheless, little information is available on sugarcane (Saccharum spp.) BBX genes and their expression profiles.

RESULTS

In the present study, we characterized 25 SsBBX genes in the Saccharum spontaneum genome database. The phylogenetic relationships, gene structures, and expression patterns of these genes during plant growth and under low-nitrogen conditions were systematically analyzed. The SsBBXs were divided into five groups based on phylogenetic analysis. The evolutionary analysis further revealed that whole-genome duplications or segmental duplications were the main driving force for the expansion of the SsBBX gene family. The expression data suggested that many BBX genes (e.g., SsBBX1 and SsBBX13) may be helpful in both plant growth and low-nitrogen stress tolerance.

CONCLUSIONS

The results of this study offer new evolutionary insight into the BBX family members in how sugarcane grows and responds to stress, which will facilitate their utilization in cultivated sugarcane breeding.

Multi-layered roles of BBX proteins in plant growth and development

Light and phytohormone are external and internal cues that regulate plant growth and development throughout their life cycle. BBXs (B-box domain proteins) are a group of zinc finger proteins that not only directly govern the transcription of target genes but also associate with other factors to create a meticulous regulatory network to precisely regulate numerous aspects of growth and developmental processes in plants. Recent studies demonstrate that BBXs play pivotal roles in light-controlled plant growth and development. Besides, BBXs have been documented to regulate phytohormone-mediated physiological procedures. In this review, we summarize and highlight the multi-faced role of BBXs, with a focus in photomorphogenesis, photoperiodic flowering, shade avoidance, abiotic stress, and phytohormone-mediated growth and development in plant.

Genome-wide identification of BBX gene family and their expression patterns under salt stress in soybean

BACKGROUND

BBX genes are key players in the regulation of various developmental processes and stress responses, which have been identified and functionally characterized in many plant species. However, our understanding of BBX family was greatly limited in soybean.

RESULTS

In this study, 59 BBX genes were identified and characterized in soybean, which can be phylogenetically classified into 5 groups. GmBBXs showed diverse gene structures and motif compositions among the groups and similar within each group. Noticeably, synteny analysis suggested that segmental duplication contributed to the expansion of GmBBX family. Moreover, our RNA-Seq data indicated that 59 GmBBXs showed different transcript profiling under salt stress, and qRT-PCR analysis confirmed their expression patterns. Among them, 22 GmBBXs were transcriptionally altered with more than two-fold changes by salt stress, supporting that GmBBXs play important roles in soybean tolerance to salt stress. Additionally, Computational assay suggested that GmBBXs might potentially interact with GmGI3, GmTOE1b, GmCOP1, GmCHI and GmCRY, while eight types of transcription factors showed potentials to bind the promoter regions of GmBBX genes.

CONCLUSIONS

Fifty-nine BBX genes were identified and characterized in soybean, and their expression patterns under salt stress and computational assays suggested their functional roles in response to salt stress. These findings will contribute to future research in regard to functions and regulatory mechanisms of soybean BBX genes in response to salt stress.

Genome-Wide Identification and Characterization of the CCT Gene Family in Foxtail Millet (Setaria italica) Response to Diurnal Rhythm and Abiotic Stress

The CCT gene family plays important roles in diurnal rhythm and abiotic stress response, affecting crop growth and development, and thus yield. However, little information is available on the CCT family in foxtail millet (Setaria italica). In the present study, we identified 37 putative SiCCT genes from the foxtail millet genome. A phylogenetic tree was constructed from the predicted full-length SiCCT amino acid sequences, together with CCT proteins from rice and Arabidopsis as representatives of monocotyledonous and dicotyledonous plants, respectively. Based on the conserved structure and phylogenetic relationships, 13, 5, and 19 SiCCT proteins were classified in the COL, PRR, and CMF subfamilies, respectively. The gene structure and protein conserved motifs analysis exhibited highly similar compositions within the same subfamily. Whole-genome duplication analysis indicated that segmental duplication events played an important role in the expansion of the CCT gene family in foxtail millet. Analysis of transcriptome data showed that 16 SiCCT genes had significant diurnal rhythm oscillations. Under abiotic stress and exogenous hormonal treatment, the expression of many CMF subfamily genes was significantly changed. Especially after drought treatment, the expression of CMF subfamily genes except SiCCT32 was significantly up-regulated. This work provides valuable information for further study of the molecular mechanism of diurnal rhythm regulation, abiotic stress responses, and the identification of candidate genes for foxtail millet molecular breeding.

Meta-analysis of QTLs and candidate genes associated with seed germination in rice (Oryza sativa L.)

Seed germination is one of the critical stages of plant life, and many quantitative trait loci (QTLs) control this complex trait. Meta-analysis of QTLs is a powerful computational technique for estimating the most stable QTLs regardless of the population's genetic background. Besides, this analysis effectively narrows down the confidence interval (CI) to identify candidate genes (CGs) and marker development. In the current study, a comprehensive genome-wide meta-analysis was performed on QTLs associated with germination in rice. This analysis was conducted based on the data reported over the last two decades. In this case, various analyses were performed, including seed germination rate, plumule length, radicle length, germination percentage, coleoptile length, coleorhiza length, radicle fresh weight, germination potential, and germination index. A total of 67 QTLs were projected onto a reference map for these traits and then integrated into 32 meta-QTLs (MQTLs) to provide a genetic framework for seed germination. The average CI of MQTLs was considerably reduced from 15.125 to 8.73 cM compared to the initial QTLs. This situation identified 728 well-known functionally characterized genes and novel putative CGs for investigated traits. The fold change calculation demonstrated that 155 CGs had significant changes in expression analysis. In this case, 112 and 43 CGs were up-regulated and down-regulated during germination, respectively. This study provides an overview and compares genetic loci controlling traits related to seed germination in rice. The findings can bridge the gap between QTLs and CGs for seed germination.

Supplementary Information

The online version contains supplementary material available at 10.1007/s12298-022-01232-1.

Rice and Arabidopsis BBX proteins: toward genetic engineering of abiotic stress resistant crops

Productivity of crop plants are enormously affected by biotic and abiotic stresses. The co-occurrence of several abiotic stresses may lead to death of crop plants. Hence, it is the responsibility of plant scientists to develop crop plants equipped with multistress tolerance pathways. A subgroup of zinc finger transcription factor family, known as B-box (BBX) proteins, play a key role in light and hormonal regulation pathways. In addition, BBX proteins act as key regulatory proteins in many abiotic stress regulatory pathways, including Ultraviolet-B (UV-B), salinity, drought, heat and cold, and heavy metal stresses. Most of the BBX proteins identified in Arabidopsis and rice respond to more than one abiotic stress. Considering the requirement of improving rice for multistress tolerance, this review discusses functionally characterized Arabidopsis and rice BBX proteins in the development of abiotic stress responses. Furthermore, it highlights the participation of BBX proteins in multistress regulation and crop improvement through genetic engineering.

Comparative Transcriptomic Analyses of Nitrate-Response in Rice Genotypes With Contrasting Nitrogen Use Efficiency Reveals Common and Genotype-Specific Processes, Molecular Targets and Nitrogen Use Efficiency-Candidates

The genetic basis for nitrogen (N)-response and N use efficiency (NUE) must be found in N-responsive gene expression or protein regulation. Our transcriptomic analysis of nitrate response in two contrasting rice genotypes of Oryza sativa ssp. Indica (Nidhi with low NUE and Panvel1 with high NUE) revealed the processes/functions underlying differential N-response/NUE. The microarray analysis of low nitrate response (1.5 mM) relative to normal nitrate control (15 mM) used potted 21-days old whole plants. It revealed 1,327 differentially expressed genes (DEGs) exclusive to Nidhi and 666 exclusive to Panvel1, apart from 70 common DEGs, of which 10 were either oppositely expressed or regulated to different extents. Gene ontology analyses revealed that photosynthetic processes were among the very few processes common to both the genotypes in low N response. Those unique to Nidhi include cell division, nitrogen utilization, cytoskeleton, etc. in low N-response, whereas those unique to Panvel1 include signal transduction, protein import into the nucleus, and mitochondria. This trend of a few common but mostly unique categories was also true for transporters, transcription factors, microRNAs, and post-translational modifications, indicating their differential involvement in Nidhi and Panvel1. Protein-protein interaction networks constructed using DEG-associated experimentally validated interactors revealed subnetworks involved in cytoskeleton organization, cell wall, etc. in Nidhi, whereas in Panvel1, it was chloroplast development. NUE genes were identified by selecting yield-related genes from N-responsive DEGs and their co-localization on NUE-QTLs revealed the differential distribution of NUE-genes between genotypes but on the same chromosomes 1 and 3. Such hotspots are important for NUE breeders.

Genome-wide identification and expression analysis of CPP-like gene family in Triticum aestivum L. under different hormone and stress conditions

The CPP-like plant‐specific transcription factor has a prominent role in plant development and growth through cell division and differential activities. However, little information is available about the CPP gene family in Triticum aestivum L. Herein, we identified 37 and 11 CPP genes in the wheat and rice genome databases, respectively. The phylogeny of the CPP protein-like family members was further divided into five subfamilies based on structural similarities and phenotypic functional diversities. The in silico expression analysis showed that CPP genes are highly expressed in some tissues, such as shoot apex, shoot, leaf, leaf sheath, and microspore. Furthermore, the qRT-PCR found higher expression for TaCPP gene family members in leaf, leaf blade, young spike, mature spike, and differential expression patterns under abiotic stresses, including heat, drought, salt, and hormonal treatment, such as indole acetic acid and 1-aminocyclopropane-1 carboxylic acid. We found that CPP gene family members are mostly located in the nucleus after infiltrating the CPP5-1B-GFP and TaCPP11-3B-GFP into tobacco leaves. The overexpression of the TaCPP5-1D gene revealed that the CPP gene positively regulates the germanium, shoot, and root activities in Arabidopsis. The TaCPP5-1D-overexpressed plants showed less anti-oxidative sensitivity under drought stress conditions. These results demonstrated that TaCPP5-1D protein has a crucial contribution by interacting with TaCPP11-3B protein in maintaining stress homeostasis under the natural and unfavorable environmental conditions for growth, development, and stress resistance activities. Therefore, this study could be used as pioneer knowledge to further investigate the function of CPP genes in plant growth and development.

Genome-Wide Characterization Analysis of CCT Genes in Raphanus sativus and Their Potential Role in Flowering and Abiotic Stress Response

CCT genes play vital roles in flowering, plant growth, development, and response to abiotic stresses. Although they have been reported in many plants, the characterization and expression pattern of CCT genes is still limited in R. sativus. In this study, a total of 58 CCT genes were identified in R. sativus. Phylogenetic tree, gene structure, and conserved domains revealed that all CCT genes were classified into three groups: COL, CMF, and PRR. Genome-wide identification and evolutionary analysis showed that segmental duplication expanded the CCT gene families considerably, with the LF subgenome retaining more CCT genes. We observed strong purifying selection pressure for CCT genes. RsCCT genes showed tissue specificity, and some genes (such as RsCCT22, RsCCT36, RsCCT42 and RsCCT51) were highly expressed in flowers. Promoter cis-elements and RNA-seq data analysis showed that RsCCT genes could play roles in controlling flowering through the photoperiodic pathway and vernalization pathway. The expression profiles of RsCCT genes under Cd, Cr, Pb, and heat and salt stresses revealed that many RsCCT genes could respond to one or more abiotic stresses. Our findings could provide essential information for further studies on the function of RsCCT genes.

Regulatory Role of Circadian Clocks on ABA Production and Signaling, Stomatal Responses, and Water-Use Efficiency under Water-Deficit Conditions

Plants deploy molecular, physiological, and anatomical adaptations to cope with long-term water-deficit exposure, and some of these processes are controlled by circadian clocks. Circadian clocks are endogenous timekeepers that autonomously modulate biological systems over the course of the day–night cycle. Plants’ responses to water deficiency vary with the time of the day. Opening and closing of stomata, which control water loss from plants, have diurnal responses based on the humidity level in the rhizosphere and the air surrounding the leaves. Abscisic acid (ABA), the main phytohormone modulating the stomatal response to water availability, is regulated by circadian clocks. The molecular mechanism of the plant’s circadian clock for regulating stress responses is composed not only of transcriptional but also posttranscriptional regulatory networks. Despite the importance of regulatory impact of circadian clock systems on ABA production and signaling, which is reflected in stomatal responses and as a consequence influences the drought tolerance response of the plants, the interrelationship between circadian clock, ABA homeostasis, and signaling and water-deficit responses has to date not been clearly described. In this review, we hypothesized that the circadian clock through ABA directs plants to modulate their responses and feedback mechanisms to ensure survival and to enhance their fitness under drought conditions. Different regulatory pathways and challenges in circadian-based rhythms and the possible adaptive advantage through them are also discussed.

The BBX gene CmBBX22 negatively regulates drought stress tolerance in chrysanthemum

BBX transcription factors play vital roles in plant growth, development, and stress responses. Although BBX proteins have been studied in great detail in the model plant Arabidopsis, their roles in crop plants such as chrysanthemum are still largely uninvestigated. Here, we cloned CmBBX22 and further determined the function of CmBBX22 in response to drought treatment. Subcellular localization and transactivation assay analyses revealed that CmBBX22 was localized in the nucleus and possessed transactivation activity. Overexpression of CmBBX22 in chrysanthemum was found to reduce plant drought tolerance, whereas expression of the chimeric repressor CmBBX22-SRDX was found to promote a higher drought tolerance than that shown by wild-type plants, indicating that CmBBX22 negatively regulates drought tolerance in chrysanthemum. Transcriptome analysis and physiological measurements indicated the potential involvement of the CmBBX22-mediated ABA response, stomatal conductance, and antioxidant responses in the negative regulation of drought tolerance in chrysanthemum. Based on the findings of this study, we were thus able to establish the mechanisms whereby the transcriptional activator CmBBX22 negatively regulates drought tolerance in chrysanthemum via the regulation of the abscisic acid response, stomatal conductance, and antioxidant responses.

Increase in Phytoextraction Potential by Genome Editing and Transformation: A Review

Soil metal contamination associated with productive activities is a global issue. Metals are not biodegradable and tend to accumulate in soils, posing potential risks to surrounding ecosystems and human health. Plant-based techniques (phytotechnologies) for the in situ remediation of metal-polluted soils have been developed, but these have some limitations. Phytotechnologies are a group of technologies that take advantage of the ability of certain plants to remediate soil, water, and air resources to rehabilitate ecosystem services in managed landscapes. Regarding soil metal pollution, the main objectives are in situ stabilization (phytostabilization) and the removal of contaminants (phytoextraction). Genetic engineering strategies such as gene editing, stacking genes, and transformation, among others, may improve the phytoextraction potential of plants by enhancing their ability to accumulate and tolerate metals and metalloids. This review discusses proven strategies to enhance phytoextraction efficiency and future perspectives on phytotechnologies.

The highly interactive BTB domain targeting other functional domains to diversify the function of BTB proteins in rice growth and development

The BTB (broad-complex, tram track, and bric-abrac) proteins are involved in developmental processes, biotic, and abiotic stress responses in various plants, but the molecular basis of protein interactions is yet to be investiagted in rice. In this study, the identified BTB proteins were divided into BTB-TAZ, MATH-BTB, BTB-NPH, BTB-ANK, BTB-Skp, BTB-DUF, and BTB-TPR subfamilies based on the additional functional domains found together with the BTB domain at N- and C-terminal as well. This suggesting that the extension region at both terminal sites could play a vital role in the BTB gene family expansion in plants. The yeast two-hybrid system, firefly luciferase complementation imaging (LCI) assay and bimolecular fluorescence complementation (BiFC) assay further confirmed that BTB proteins interact with several other proteins to perform a certain developmental process in plants. The overexpression of BTB genes of each subfamily in Arabidopsis revealed that BTB genes including OsBTB4, OsBTB8, OsBTB64, OsBTB62, OsBTB138, and OsBTB147, containing certain additional functional domains, could play a potential role in the early flowering, branching, leaf, and silique development. Thus we concluded that the presence of other functional domains such as TAZ, SKP, DUF, ANK, NPH, BACK, PQQ, and MATH could be the factor driving the diverse functions of BTB proteins in plant biology.

Genome-Wide Identification, Evolution, and Comparative Analysis of B-Box Genes in Brassica rapa, B. oleracea, and B. napus and Their Expression Profiling in B. rapa in Response to Multiple Hormones and Abiotic Stresses

The B-box zinc-finger transcription factors are important for plant growth, development, and various physiological processes such as photomorphogenesis, light signaling, and flowering, as well as for several biotic and abiotic stress responses. However, there is relatively little information available regarding Brassica B-box genes and their expression. In this study, we identified 51, 52, and 101 non-redundant genes encoding B-box proteins in Brassica rapa (BrBBX genes), B. oleracea (BoBBX genes), and B. napus (BnBBX genes), respectively. A whole-genome identification, characterization, and evolutionary analysis (synteny and orthology) of the B-box gene families in the diploid species B. rapa (A genome) and B. oleracea (C genome) and in the allotetraploid species B. napus (AC genome) revealed segmental duplications were the major contributors to the expansion of the BrassicaBBX gene families. The BrassicaBBX genes were classified into five subgroups according to phylogenetic relationships, gene structures, and conserved domains. Light-responsive cis-regulatory elements were detected in many of the BBX gene promoters. Additionally, BrBBX expression profiles in different tissues and in response to various abiotic stresses (heat, cold, salt, and drought) or hormones (abscisic acid, methyl jasmonate, and gibberellic acid) were analyzed by qRT-PCR. The data indicated that many B-box genes (e.g., BrBBX13, BrBBX15, and BrBBX17) may contribute to plant development and growth as well as abiotic stress tolerance. Overall, the identified BBX genes may be useful as functional genetic markers for multiple stress responses and plant developmental processes.

CpBBX19, a B-Box Transcription Factor Gene of Chimonanthus praecox, Improves Salt and Drought Tolerance in Arabidopsis

Zinc-finger proteins are important transcription factors in plants, responding to adversity and regulating the growth and development of plants. However, the roles of the BBX gene family of zinc-finger proteins in wintersweet (Chimonanthus praecox) have yet to be elucidated. In this study, a group IV subfamily BBX gene, CpBBX19, was identified and isolated from wintersweet. Quantitative real-time PCR (qRT-PCR) analyses revealed that CpBBX19 was expressed in all tissues and that expression was highest in cotyledons and inner petals. CpBBX19 was also expressed in all flower development stages, with the highest expression detected in early initiating bloom, followed by late initiating bloom and bloom. In addition, the expression of CpBBX19 was induced by different abiotic stress (cold, heat, NaCl, and drought) and hormone (ABA and MeJA) treatments. Heterologous expression of CpBBX19 in Arabidopsis thaliana (Arabidopsis) enhanced the tolerance of this plant to salt and drought stress as electrolyte leakage and malondialdehyde (MDA) concentrations in transgenic Arabidopsis after stress treatments were significantly lower than those in wild-type (WT) plants. In conclusion, this research demonstrated that CpBBX19 plays a role in the abiotic stress tolerance of wintersweet. These findings lay a foundation for future studies on the BBX gene family of wintersweet and enrich understanding of the molecular mechanism of stress resistance in wintersweet.

A poplar B-box protein PtrBBX23 modulates the accumulation of anthocyanins and proanthocyanidins in response to high light

Flavonoids, which modulate plant resistance to various stresses, can be induced by high light. B-box (BBX) transcription factors (TFs) play crucial roles in the transcriptional regulation of flavonoids biosynthesis, but limited information is available on the association of BBX proteins with high light. We present a detailed overview of 45 Populus trichocarpa BBX TFs. Phylogenetic relationships, gene structure, tissue-specific expression patterns and expression profiles were determined under 10 stress or phytohormone treatments to screen candidate BBX proteins associated with the flavonoid pathway. Sixteen candidate genes were identified, of which five were expressed predominantly in young leaves and roots, and BBX23 showed the most distinct response to high light. Overexpression of BBX23 in poplar activated expression of MYB TFs and structural genes in the flavonoid pathway, thereby promoting the accumulation of proanthocyanidins and anthocyanins. CRISPR/Cas9-generated knockout of BBX23 resulted in the opposite trend. Furthermore, the phenotype induced by BBX23 overexpression was enhanced under exposure to high light. BBX23 was capable of binding directly to the promoters of proanthocyanidin- and anthocyanin-specific genes, and its interaction with HY5 enhanced activation activity. We identified novel regulators of flavonoid biosynthesis in poplar, thereby enhancing our general understanding of the transcriptional regulatory mechanisms involved.

The BBX gene family in Moso bamboo (Phyllostachys edulis): identification, characterization and expression profiles

BACKGROUND

The BBX (B-box) family are zinc finger protein (ZFP) transcription factors that play an essential role in plant growth, development and response to abiotic stresses. Although BBX genes have been characterized in many model organisms, genome-wide identification of the BBX family genes have not yet been reported in Moso bamboo (Phyllostachys edulis), and the biological functions of this family remain unknown.

RESULT

In the present study, we identified 27 BBX genes in the genome of Moso bamboo, and analysis of their conserved motifs and multiple sequence alignments revealed that they all shared highly similar structures. Additionally, phylogenetic and homology analyses indicated that PeBBX genes were divided into three clusters, with whole-genome duplication (WGD) events having facilitated the expansion of this gene family. Light-responsive and stress-related cis-elements were identified by analyzing cis-elements in the promoters of all PeBBX genes. Short time-series expression miner (STEM) analysis revealed that the PeBBX genes had spatiotemporal-specific expression patterns and were likely involved in the growth and development of bamboo shoots. We further explored the downstream target genes of PeBBXs, and GO/KEGG enrichment analysis predicted multiple functions of BBX target genes, including those encoding enzymes involved in plant photosynthesis, pyruvate metabolism and glycolysis/gluconeogenesis.

CONCLUSIONS

In conclusion, we analyzed the PeBBX genes at multiple different levels, which will contribute to further studies of the BBX family and provide valuable information for the functional validation of this family.

Genome-wide identification of Brassicaceae B-BOX genes and molecular characterization of their transcriptional responses to various nutrient stresses in allotetraploid rapeseed

BACKGROUND

B-box (BBX) genes play important roles in plant growth regulation and responses to abiotic stresses. The plant growth and yield production of allotetraploid rapeseed is usually hindered by diverse nutrient stresses. However, no systematic analysis of Brassicaceae BBXs and the roles of BBXs in the regulation of nutrient stress responses have not been identified and characterized previously.

RESULTS

In this study, a total of 536 BBXs were identified from nine brassicaceae species, including 32 AtBBXs, 66 BnaBBXs, 41 BoBBXs, 43 BrBBXs, 26 CrBBXs, 81 CsBBXs, 52 BnBBXs, 93 BjBBXs, and 102 BcBBXs. Syntenic analysis showed that great differences in the gene number of Brassicaceae BBXs might be caused by genome duplication. The BBXs were respectively divided into five subclasses according to their phylogenetic relationships and conserved domains, indicating their diversified functions. Promoter cis-element analysis showed that BBXs probably participated in diverse stress responses. Protein-protein interactions between BnaBBXs indicated their functions in flower induction. The expression profiles of BnaBBXs were investigated in rapeseed plants under boron deficiency, boron toxicity, nitrate limitation, phosphate shortage, potassium starvation, ammonium excess, cadmium toxicity, and salt stress conditions using RNA-seq data. The results showed that different BnaBBXs showed differential transcriptional responses to nutrient stresses, and some of them were simultaneously responsive to diverse nutrient stresses.

CONCLUSIONS

Taken together, the findings investigated in this study provided rich resources for studying Brassicaceae BBX gene family and enriched potential clues in the genetic improvement of crop stress resistance.

The TAZ domain-containing proteins play important role in the heavy metals stress biology in plants

TAZ (transcriptional coactivator with PDZ-binding) zinc finger domains, also known as transcription adaptor putative zinc finger domains, that control diverse function in plant growth and development. Here, in the present study, we evaluated the role of the TAZ domain-containing gene in response to various heavy metals. Initially, we found a total of 3, 7, 8, 9, 9, 9, 7, 14, 6, 10, and 6 proteins containing TAZ domain in stiff brome, millet, sorghum, potato, pepper, maize, rice, apple, peach, pear, and tomato genome that could trigger the plant resistance against various heavy metals, respectively. Various in-silico approaches were applied such as duplication, phylogenetic analysis, and gene structure, to understand the basic features of the TAZ domain-containing genes in plants. Gene expression analyses were also performed under heavy metals (Cr, Zn, Ni, Cd, Co, Fe, Mn, and Pb). The results of quantitative real-time PCR analysis indicated that the TAZ gene family members were differentially expressed under different heavy metals. We further characterized the functions of the TAZ domain-containing gene under the heavy metal stresses by overexpressing the OsTAZ4 gene in Arabidopsis. The TAZ genes could promote plant resistance against various heavy metals by interacting with OsMYB34 and OsFHA9 transcription factors. The results will contribute to elucidate the relationship of TAZ proteins with heavy metals stresses and also ascertain the biological function in plant growth and development.

Genome-wide identification and expression analysis of the B-box transcription factor gene family in grapevine (Vitis vinifera L.)

Background

B-box (BBX) zinc-finger transcription factors play important roles in plant growth, development, and stress response. Although these proteins have been studied in model plants such as Arabidopsis thaliana or Oryza sativa, little is known about the evolutionary history or expression patterns of BBX proteins in grapevine (Vitis vinifera L.).

Results

We identified a total of 25 VviBBX genes in the grapevine genome and named them according to the homology with Arabidopsis. These proteins were classified into five groups on the basis of their phylogenetic relationships, number of B-box domains, and presence or absence of a CCT domain or VP motif. BBX proteins within the same group showed similar exon-intron structures and were unevenly distributed in grapevine chromosomes. Synteny analyses suggested that only segmental duplication events contributed to the expansion of the VviBBX gene family in grapevine. The observed syntenic relationships between some BBX genes from grapevine and Arabidopsis suggest that they evolved from a common ancestor. Transcriptional analyses showed that the grapevine BBX genes were regulated distinctly in response to powdery mildew infection and various phytohormones. Moreover, the expression levels of a subset of BBX genes in ovules were much higher in seedless grapevine cultivars compared with seeded cultivars during ovule development, implying a potential role in seed abortion. Additionally, VviBBX8, VquBBX15a and VquBBX29b were all located in the nucleus and had transcriptional activity except for VquBBX29b.

Conclusions

The results of this study establish the genome-wide analysis of the grapevine BBX family and provide a framework for understanding the biological roles of BBX genes in grapevine.

Supplementary Information

The online version contains supplementary material available at 10.1186/s12864-021-07479-4.

Beyond Arabidopsis: BBX Regulators in Crop Plants

B-box proteins represent diverse zinc finger transcription factors and regulators forming large families in various plants. A unique domain structure defines them—besides the highly conserved B-box domains, some B-box (BBX) proteins also possess CCT domain and VP motif. Based on the presence of these specific domains, they are mostly classified into five structural groups. The particular members widely differ in structure and fulfill distinct functions in regulating plant growth and development, including seedling photomorphogenesis, the anthocyanins biosynthesis, photoperiodic regulation of flowering, and hormonal pathways. Several BBX proteins are additionally involved in biotic and abiotic stress response. Overexpression of some BBX genes stimulates various stress-related genes and enhanced tolerance to different stresses. Moreover, there is evidence of interplay between B-box and the circadian clock mechanism. This review highlights the role of BBX proteins as a part of a broad regulatory network in crop plants, considering their participation in development, physiology, defense, and environmental constraints. A description is also provided of how various BBX regulators involved in stress tolerance were applied in genetic engineering to obtain stress tolerance in transgenic crops.

B-box Proteins in Arachis duranensis: Genome-Wide Characterization and Expression Profiles Analysis

B-box (BBX) proteins are important factors involved in plant growth and developmental regulation, and they have been identified in many species. However, information on the characteristics and transcription patterns of BBX genes in wild peanut are limited. In this study, we identified and characterized 24 BBX genes from a wild peanut, Arachis duranensis. Many characteristics were analyzed, including chromosomal locations, phylogenetic relationships, and gene structures. Arachis duranensis B-box (AdBBX) proteins were grouped into five classes based on the diversity of their conserved domains: I (3 genes), II (4 genes), III (4 genes), IV (9 genes), and V (4 genes). Fifteen distinct motifs were found in the 24 AdBBX proteins. Duplication analysis revealed the presence of two interchromosomal duplicated gene pairs, from group II and IV. In addition, 95 kinds of cis-acting elements were found in the genes’ promoter regions, 53 of which received putative functional predictions. The numbers and types of cis-acting elements varied among different AdBBX promoters, and, as a result, AdBBX genes exhibited distinct expression patterns in different tissues. Transcriptional profiling combined with synteny analysis suggests that AdBBX8 may be a key factor involved in flowering time regulation. Our study will provide essential information for further functional investigation of AdBBX genes.