Genome-Wide Analyses of the Genetic Screening of C2H2-Type Zinc Finger Transcription Factors and Abiotic and Biotic Stress Responses in Tomato (Solanum lycopersicum) Based on RNA-Seq Data

Transcriptomic Approach for Investigation of Solanum spp. Resistance upon Early-Stage Broomrape Parasitism

Tomato (Solanum lycopersicum) is a major horticultural crop of high economic importance. Phelipanche and Orobanche genera (broomrapes) are parasitic weeds, constituting biotic stressors that impact tomato production. Developing varieties with tolerance to broomrapes has become imperative for sustainable agriculture. Solanum pennellii, a wild relative of cultivated tomato, has been utilized as breeding material for S. lycopersicum. In the present study, it is the first time that an in-depth analysis has been conducted for these two specific introgression lines (ILs), IL6-2 and IL6-3 (S. lycopersicum X S. pennellii), which were employed to identify genes and metabolic pathways associated with resistance against broomrape. Comparative transcriptomic analysis revealed a multitude of differentially expressed genes (DEGs) in roots, especially in the resistant genotype IL6-3, several of which were validated by quantitative PCR. DEG and pathway enrichment analysis (PEA) revealed diverse molecular mechanisms that can potentially be implicated in the host's defense response and the establishment of resistance. The identified DEGs were mostly up-regulated in response to broomrape parasitism and play crucial roles in various processes different from strigolactone regulation. Our findings indicate that, in addition to the essential role of strigolactone metabolism, multiple cellular processes may be involved in the tomato's response to broomrapes. The insights gained from this study will enhance our understanding and facilitate molecular breeding methods regarding broomrape parasitism. Moreover, they will assist in developing sustainable strategies and providing alternative solutions for weed management in tomatoes and other agronomically important crops.

Genome-wide characterization and expression profiling of E2F/DP gene family members in response to abiotic stress in tomato (Solanum lycopersicum L.)

BACKGROUND

E2F/DP (Eukaryotic 2 transcription factor/dimerization partner) family proteins play an essential function in the cell cycle development of higher organisms. E2F/DP family genes have been reported only in a few plant species. However, comprehensive genome-wide characterization analysis of the E2F/DP gene family of Solanum lycopersicum has not been reported so far.

RESULTS

This study identified eight nonredundant SlE2F/DP genes that were classified into seven groups in the phylogenetic analysis. All eight genes had a single E2F-TDP domain and few genes had additional domains. Two segmental duplication gene pairs were observed within tomato, in addition to cis-regulatory elements, miRNA target sites and phosphorylation sites which play an important role in plant development and stress response in tomato. To explore the three-dimensional (3D) models and gene ontology (GO) annotations of SlE2F/DP proteins, we pointed to their putative transporter activity and their interaction with several putative ligands. The localization of SlE2F/DP-GFP fused proteins in the nucleus and endoplasmic reticulum suggested that they may act in other biological functions. Expression studies revealed the differential expression pattern of most of the SlE2F/DP genes in various organs. Moreover, the expression of E2F/DP genes against abiotic stress, particularly SlE2F/DP2 and/or SlE2F/DP7, was upregulated in response to heat, salt, cold and ABA treatment. Furthermore, the co-expression analysis of SlE2F/DP genes with multiple metabolic pathways was co-expressed with defence genes, transcription factors and so on, suggested their crucial role in various biological processes.

CONCLUSIONS

Overall, our findings provide a way to understand the structure and function of SlE2F/DP genes; it might be helpful to improve fruit development and tolerance against abiotic stress through marker-assisted selection or transgenic approaches.

Genome-wide analysis of C2H2 zinc finger family and their response to abiotic stresses in apple

C2H2-type zinc finger proteins are one of the most widely studied families in plants and play important roles in abiotic stress responses. In the present study, the physicochemical properties, chromosomal locations, evolutionary relationships, and gene structures of 54 C2H2 zinc finger protein (ZFP) family members were analyzed in apple. The MdC2H2-ZFP genes were phylogenetically clustered into seven subfamilies distributed in different densities on 16 chromosomes. The RNA-seq data from various tissues revealed that MdC2H2-ZFPs differentially expressed among root, stem, leaf, flower, and fruits. Quantitative analysis of its expression characteristics showed that the MdC2H2-ZFP genes were rapidly induced as exposure to abiotic stresses such as drought, salt and low temperature etc. Under drought stress, the expression of eight members was significantly up-regulated, and the highest was obtained from MdC2H2-17; as exposure to salt stress, nine MdC2H2-ZFPs was obviously up-regulated, with the highest expression of MdC2H2-13; and under low temperature stress, the expression of seven members was highly up-regulated, and MdC2H2-13 also demonstrated the highest expression which is same as the case under salt stress. Therefore, some members of MdC2H2-ZFP gene family considerably involve in the multiple abiotic stress responses, which may better understand the function of this family and facilitate the breeding of apple for stress tolerance.

The DBB Family in Populus trichocarpa: Identification, Characterization, Evolution and Expression Profiles

The B-box proteins (BBXs) encode a family of zinc-finger transcription factors that regulate the plant circadian rhythm and early light morphogenesis. The double B-box (DBB) family is in the class of the B-box family, which contains two conserved B-box domains and lacks a CCT (CO, CO-like and TOC1) motif. In this study, the identity, classification, structures, conserved motifs, chromosomal location, cis elements, duplication events, and expression profiles of the PtrDBB genes were analyzed in the woody model plant Populus trichocarpa. Here, 12 PtrDBB genes (PtrDBB1-PtrDBB12) were identified and classified into four distinct groups, and all of them were homogeneously spread among eight out of seventeen poplar chromosomes. The collinearity analysis of the DBB family genes from P. trichocarpa and two other species (Z. mays and A. thaliana) indicated that segmental duplication gene pairs and high-level conservation were identified. The analysis of duplication events demonstrates an insight into the evolutionary patterns of DBB genes. The previously published transcriptome data showed that PtrDBB genes represented distinct expression patterns in various tissues at different stages. In addition, it was speculated that several PtrDBBs are involved in the responsive to drought stress, light/dark, and ABA and MeJA treatments, which implied that they might function in abiotic stress and phytohormone responses. In summary, our results contribute to the further understanding of the DBB family and provide a reference for potential functional studies of PtrDBB genes in P. trichocarpa.

Mutagenesis-based plant breeding approaches and genome engineering: A review focused on tomato

Breeding is the most important and efficient method for crop improvement involving repeated modification of the genetic makeup of a plant population over many generations. In this review, various accessible breeding approaches, such as conventional breeding and mutation breeding (physical and chemical mutagenesis and insertional mutagenesis), are discussed with respect to the actual impact of research on the economic improvement of tomato agriculture. Tomatoes are among the most economically important fruit crops consumed worldwide because of their high nutritional content and health-related benefits. Additionally, we summarize mutation-based mapping approaches, including Mutmap and MutChromeSeq, for the efficient mapping of several genes identified by random indel mutations that are beneficial for crop improvement. Difficulties and challenges in the adaptation of new genome editing techniques that provide opportunities to demonstrate precise mutations are also addressed. Lastly, this review focuses on various effective and convenient genome editing tools, such as RNA interference (RNAi), zinc finger nucleases (ZFNs), transcription activator-like effector nucleases (TALENs), and clustered regularly interspaced short palindromic repeats (CRISPR/Cas9), and their potential for the improvement of numerous desirable traits to allow the development of better varieties of tomato and other horticultural crops.

Tomato Biodiversity and Drought Tolerance: A Multilevel Review

Ongoing global climate change suggests that crops will be exposed to environmental stresses that may affect their productivity, leading to possible global food shortages. Among these stresses, drought is the most important contributor to yield loss in global agriculture. Drought stress negatively affects various physiological, genetic, biochemical, and morphological characteristics of plants. Drought also causes pollen sterility and affects flower development, resulting in reduced seed production and fruit quality. Tomato (Solanum lycopersicum L.) is one of the most economically important crops in different parts of the world, including the Mediterranean region, and it is known that drought limits crop productivity, with economic consequences. Many different tomato cultivars are currently cultivated, and they differ in terms of genetic, biochemical, and physiological traits; as such, they represent a reservoir of potential candidates for coping with drought stress. This review aims to summarize the contribution of specific physio-molecular traits to drought tolerance and how they vary among tomato cultivars. At the genetic and proteomic level, genes encoding osmotins, dehydrins, aquaporins, and MAP kinases seem to improve the drought tolerance of tomato varieties. Genes encoding ROS-scavenging enzymes and chaperone proteins are also critical. In addition, proteins involved in sucrose and CO₂ metabolism may increase tolerance. At the physiological level, plants improve drought tolerance by adjusting photosynthesis, modulating ABA, and pigment levels, and altering sugar metabolism. As a result, we underline that drought tolerance depends on the interaction of several mechanisms operating at different levels. Therefore, the selection of drought-tolerant cultivars must consider all these characteristics. In addition, we underline that cultivars may exhibit distinct, albeit overlapping, multilevel responses that allow differentiation of individual cultivars. Consequently, this review highlights the importance of tomato biodiversity for an efficient response to drought and for preserving fruit quality levels.

Genome-Wide Identification and Expression Analysis of Cysteine-Rich Polycomb-like Protein (CPP) Gene Family in Tomato

The cysteine-rich polycomb-like protein (CPP) gene family is a class of transcription factors containing conserved cysteine-rich CRC structural domains that is involved in the regulation of plant growth and stress tolerance to adversity. Relative to other gene families, the CPP gene family has not received sufficient attention. In this study, six SlCPPs were identified for the first time using the most recent genome-wide identification data of tomato. Subsequently, a phylogenetic analysis classified SlCPPs into four subfamilies. The analysis of cis-acting elements in the promoter indicates that SlCPPs are involved in plant growth and development and also stress response. We present for the first time the prediction of the tertiary structure of these SlCPPs proteins using the AlphaFold2 artificial intelligence system developed by the DeepMind team. Transcriptome data analysis showed that SlCPPs were differentially expressed in different tissues. Gene expression profiling showed that all SlCPPs except SlCPP5 were up-regulated under drought stress; SlCPP2, SlCPP3 and SlCPP4 were up-regulated under cold stress; SlCPP2 and SlCPP5 were up-regulated under salt stress; all SlCPPs were up-regulated under inoculation with Cladosporium fulvum; and SlCPP1, SlCPP3, and SlCPP4 were up-regulated under inoculation with Stemphylium lycopersici. We performed a virus-induced gene silencing experiment on SlCPP3, and the results indicated that SlCPP3 was involved in the response to drought stress. Finally, we predicted the interaction network of the key gene SlCPP3, and there was an interaction relationship between SlCPP3 and 10 genes, such as RBR1 and MSI1. The positive outcome showed that SlCPPs responded to environmental stress. This study provides a theoretical and empirical basis for the response mechanisms of tomato in abiotic stresses.

Analysis of the C2H2 Gene Family in Maize (Zea mays L.) under Cold Stress: Identification and Expression

The C2H2 zinc finger protein is one of the most common zinc finger proteins, widely exists in eukaryotes, and plays an important role in plant growth and development, as well as in salt, low-temperature, and drought stress and other abiotic stress responses. In this study, C2H2 members were identified and analyzed from the low-temperature tolerant transcriptome sequencing data of maize seedlings. The chromosome position, physical and chemical properties, evolution analysis, gene structure, conservative motifs, promoter cis elements and collinearity relationships of gene the family members were analyzed using bioinformatics, and the expression of the ZmC2H2 gene family under cold stress was analyzed by fluorescent quantitative PCR. The results showed that 150 members of the C2H2 zinc finger protein family were identified, and their protein lengths ranged from 102 to 1223 bp. The maximum molecular weight of the ZmC2H2s was 135,196.34, and the minimum was 10,823.86. The isoelectric point of the ZmC2H2s was between 33.21 and 94.1, and the aliphatic index was 42.07-87.62. The promoter cis element analysis showed that the ZmC2H2 family contains many light-response elements, plant hormone-response elements, and stress-response elements. The analysis of the transcriptome data showed that most of the ZmC2H2 genes responded to cold stress, and most of the ZmC2H2 genes were highly expressed in cold-tolerant materials and lowly expressed in cold-sensitive materials. The real-time quantitative PCR (qRT-PCR) analysis showed that ZmC2H2-69, ZmC2H2-130, and ZmC2H2-76 were significantly upregulated, and that ZmC2H2-149, ZmC2H2-33, and ZmC2H2-38 were significantly downregulated. It is hypothesized that these genes, which function in different metabolic pathways, may play a key role in the maize cold response. These genes could be further studied as candidate genes. This study provides a theoretical reference for further study on the function analysis of the maize C2H2 gene family.

Genome-Wide Identification of C2H2 ZFPs and Functional Analysis of BRZAT12 under Low-Temperature Stress in Winter Rapeseed (Brassica rapa)

Zinc-finger protein (ZFP) transcription factors are among the largest families of transcription factors in plants. They participate in various biological processes such as apoptosis, autophagy, and stemness maintenance and play important roles in regulating plant growth and development and the response to stress. To elucidate the functions of ZFP genes in the low-temperature response of winter (Brassica rapa L.) B. rapa, this study identified 141 members of the C2H2 ZFP gene family from B. rapa, which are heterogeneously distributed on 10 chromosomes and have multiple cis-acting elements related to hormone regulation and abiotic stress of adversity. Most of the genes in this family contain only one CDS, and genes distributed in the same evolutionary branch share mostly the same motifs and are highly conserved in the evolution of cruciferous species. The genes were significantly upregulated in the roots and growth cones of ‘Longyou-7’, indicating that they play a role in the stress-response process of winter B. rapa. The expression level of the Bra002528 gene was higher in the strongly cold-resistant varieties than in the weakly cold-resistant varieties after low-temperature stress. The survival rate and BrZAT12 gene expression of trans-BrZAT12 Arabidopsis thaliana (Arabidopsis) were significantly higher than those of the wild-type plants at low temperature, and the enzyme activities in vivo were higher than those of the wild-type plants, indicating that the BrZAT12 gene could improve the cold resistance of winter B. rapa. BrZAT12 expression and superoxide dismutase and ascorbate peroxidase enzyme activities were upregulated in winter B. rapa after exogenous ABA treatment. BrZAT12 expression and enzyme activities decreased after the PD98059 treatment, and BrZAT12 expression and enzyme activities were higher than in the PD98059 treatment but lower than in the control after both treatments together. It is speculated that BrZAT12 plays a role in the ABA signaling process in which MAPKK is involved. This study provides a theoretical basis for the resolution of cold-resistance mechanisms in strong winter B. rapa.

Genome-Wide Identification and Expression Analysis of the Zinc Finger Protein Gene Subfamilies under Drought Stress in Triticum aestivum

The zinc finger protein (ZFP) family is one of plants’ most diverse family of transcription factors. These proteins with finger-like structural domains have been shown to play a critical role in plant responses to abiotic stresses such as drought. This study aimed to systematically characterize Triticum aestivum ZFPs (TaZFPs) and understand their roles under drought stress. A total of 9 TaC2H2, 38 TaC3HC4, 79 TaCCCH, and 143 TaPHD were identified, which were divided into 4, 7, 12, and 14 distinct subgroups based on their phylogenetic relationships, respectively. Segmental duplication dominated the evolution of four subfamilies and made important contributions to the large-scale amplification of gene families. Syntenic relationships, gene duplications, and Ka/Ks result consistently indicate a potential strong purifying selection on TaZFPs. Additionally, TaZFPs have various abiotic stress-associated cis-acting regulatory elements and have tissue-specific expression patterns showing different responses to drought and heat stress. Therefore, these genes may play multiple functions in plant growth and stress resistance responses. This is the first comprehensive genome-wide analysis of ZFP gene families in T. aestivum to elucidate the basis of their function and resistance mechanisms, providing a reference for precise manipulation of genetic engineering for drought resistance in T. aestivum.

Genome-wide analysis of the C2H2 zinc finger protein gene family and its response to salt stress in ginseng, Panax ginseng Meyer

The C2H2 zinc finger protein (C2H2-ZFP) gene family plays important roles in response to environmental stresses and several other biological processes in plants. Ginseng is a precious medicinal herb cultivated in Asia and North America. However, little is known about the C2H2-ZFP gene family and its functions in ginseng. Here, we identified 115 C2H2-ZFP genes from ginseng, defined as the PgZFP gene family. It was clustered into five groups and featured with eight conserved motifs, with each gene containing one to six of them. The family genes are categorized into 17 gene ontology subcategories and have numerous regulatory elements responsive to a variety of biological process, suggesting their functional differentiation. The 115 PgZFP genes were spliced into 228 transcripts at seed setting stage and varied dramatically in expression across tissues, developmental stages, and genotypes, but they form a co-expression network, suggesting their functional correlation. Furthermore, four genes, PgZFP31, PgZFP78-01, PgZFP38, and PgZFP39-01, were identified from the gene family that were actively involved in plant response to salt stress. These results provide new knowledge on origin, differentiation, evolution, and function of the PgZFP gene family and new gene resources for C2H2-ZFP gene research and application in ginseng and other plant species.

Drought tolerance improvement in Solanum lycopersicum: an insight into "OMICS" approaches and genome editing

Solanum lycopersicum (tomato) is an internationally acclaimed vegetable crop that is grown worldwide. However, drought stress is one of the most critical challenges for tomato production, and it is a crucial task for agricultural biotechnology to produce drought-resistant cultivars. Although breeders have done a lot of work on the tomato to boost quality and quantity of production and enhance resistance to biotic and abiotic stresses, conventional tomato breeding approaches have been limited to improving drought tolerance because of the intricacy of drought traits. Many efforts have been made to better understand the mechanisms involved in adaptation and tolerance to drought stress in tomatoes throughout the years. "Omics" techniques, such as genomics, transcriptomics, proteomics, and metabolomics in combination with modern sequencing technologies, have tremendously aided the discovery of drought-responsive genes. In addition, the availability of biotechnological tools, such as plant transformation and the recently developed genome editing system for tomatoes, has opened up wider opportunities for validating the function of drought-responsive genes and the generation of drought-tolerant varieties. This review highlighted the recent progresses for tomatoes improvement against drought stress through "omics" and "multi-omics" technologies including genetic engineering. We have also discussed the roles of non-coding RNAs and genome editing techniques for drought stress tolerance improvement in tomatoes.

A Xanthomonas transcription activator-like effector is trapped in nonhost plants for immunity

Xanthomonas oryzae pv. oryzae (Xoo), the causal agent of bacterial leaf blight in rice, delivers transcription activator-like effector (TALE) proteins into host cells to activate susceptibility or resistance (R) genes that promote disease or immunity, respectively. Nonhost plants serve as potential reservoirs of R genes; consequently, nonhost R genes may trap TALEs to trigger an immune response. In this study, we screened 17 Xoo TALEs for their ability to induce a hypersensitive response (HR) in the nonhost plant Nicotiana benthamiana (Nb); only AvrXa10 elicited an HR when transiently expressed in Nb. The HR generated by AvrXa10 required both the central repeat region and the activation domain, suggesting a specific interaction between AvrXa10 and a potential R-like gene in nonhost plants. Evans blue staining and ion leakage measurements confirmed that the AvrXa10-triggered HR was a form of cell death, and the transient expression of AvrXa10 in Nb induced immune responses. Genes targeted by AvrXa10 in the Nb genome were identified by transcriptome profiling and prediction of effector binding sites. Using several approaches (in vivo reporter assays, electrophoretic mobility-shift assays, targeted designer TALEs, and on-spot gene silencing), we confirmed that AvrXa10 targets NbZnFP1, a C2H2-type zinc finger protein that resides in the nucleus. Functional analysis indicated that overexpression of NbZnFP1 and its rice orthologs triggered cell death in rice protoplasts. An NbZnFP1 ortholog was also identified in tomato and was specifically activated by AvrXa10. These results demonstrate that NbZnFP1 is a nonhost R gene that traps AvrXa10 to promote plant immunity in Nb.

Integrated transcriptome and small RNA sequencing analyses reveal a drought stress response network in Sophora tonkinensis

BACKGROUND

Sophora tonkinensis Gagnep is a traditional Chinese medical plant that is mainly cultivated in southern China. Drought stress is one of the major abiotic stresses that negatively impacts S. tonkinensis growth. However, the molecular mechanisms governing the responses to drought stress in S. tonkinensis at the transcriptional and posttranscriptional levels are not well understood.

RESULTS

To identify genes and miRNAs involved in drought stress responses in S. tonkinensis, both mRNA and small RNA sequencing was performed in root samples under control, mild drought, and severe drought conditions. mRNA sequencing revealed 66,476 unigenes, and the differentially expressed unigenes (DEGs) were associated with several key pathways, including phenylpropanoid biosynthesis, sugar metabolism, and quinolizidine alkaloid biosynthesis pathways. A total of 10 and 30 transcription factors (TFs) were identified among the DEGs under mild and severe drought stress, respectively. Moreover, small RNA sequencing revealed a total of 368 miRNAs, including 255 known miRNAs and 113 novel miRNAs. The differentially expressed miRNAs and their target genes were involved in the regulation of plant hormone signal transduction, the spliceosome, and ribosomes. Analysis of the regulatory network involved in the response to drought stress revealed 37 differentially expressed miRNA-mRNA pairs.

CONCLUSION

This is the first study to simultaneously profile the expression patterns of mRNAs and miRNAs on a genome-wide scale to elucidate the molecular mechanisms of the drought stress responses of S. tonkinensis. Our results suggest that S. tonkinensis implements diverse mechanisms to modulate its responses to drought stress.

Advances in the Regulation of Epidermal Cell Development by C2H2 Zinc Finger Proteins in Plants

Plant epidermal cells, such as trichomes, root hairs, salt glands, and stomata, play pivotal roles in the growth, development, and environmental adaptation of terrestrial plants. Cell fate determination, differentiation, and the formation of epidermal structures represent basic developmental processes in multicellular organisms. Increasing evidence indicates that C2H2 zinc finger proteins play important roles in regulating the development of epidermal structures in plants and plant adaptation to unfavorable environments. Here, we systematically summarize the molecular mechanism underlying the roles of C2H2 zinc finger proteins in controlling epidermal cell formation in plants, with an emphasis on trichomes, root hairs, and salt glands and their roles in plant adaptation to environmental stress. In addition, we discuss the possible roles of homologous C2H2 zinc finger proteins in trichome development in non-halophytes and salt gland development in halophytes based on bioinformatic analysis. This review provides a foundation for further study of epidermal cell development and abiotic stress responses in plants.

Global proteome response to Pb(II) toxicity in poplar using SWATH-MS-based quantitative proteomics investigation

Lead (Pb) toxicity is a growing serious environmental pollution that threatens human health and crop productivity. Poplar, as an important economic and ecological forest species, has the characteristics of fasting growth and accumulating heavy metals, which is a powerful model plant for phytoremediation. Here, a novel label-free quantitative proteomic platform of SWATH-MS was applied to detect proteome changes in poplar seedling roots following Pb treatment. In total 4388 unique proteins were identified and quantified, among which 542 proteins showed significant abundance changes upon Pb(II) exposure. Functional categorizations revealed that differentially expressed proteins (DEPs) primarily distributed in specialized biological processes. Particularly, lignin and flavonoid biosynthesis pathway were strongly activated upon Pb exposure, implicating their potential roles for Pb detoxification in poplar. Furthermore, hemicellulose and pectin related cell wall proteins exhibited increased abundances, where may function as a sequestration reservoir to reduce Pb toxicity in cytoplasm. Simultaneously, up-regulation of glutathione metabolism may serve as a protective role for Pb-induced oxidative damages in poplar. Further correlation investigation revealed an extra layer of post-transcriptional regulation during Pb response in poplar. Overall, our work represents multiply potential regulators in mediating Pb tolerance in poplar, providing molecular targets and strategies for phytoremediation.

Identification of C2H2 subfamily ZAT genes in Gossypium species reveals GhZAT34 and GhZAT79 enhanced salt tolerance in Arabidopsis and cotton

Soil salinization is a vital factor that restricts the efficient and sustainable development of global agriculture. Studies enlightened that the C₂H₂ zinc finger proteins (C₂H₂-ZFP) were involved in regulating the stress response in plants. However, knowledge of the C₂H₂-ZFP subfamily C1 (ZAT; Zinc finger of Arabidopsis thaliana) in cotton is still a mystery. In this study, 47, 45, 94, and 88 ZAT genes were obtained from diploid A2, D5 and tetraploid AD1, AD2 cotton genomes, respectively. The function of hybridization and allopolyploidy in the evolutionary linkage of allotetraploid cotton was explained by the family of ZAT gene in 4 species. Duplication of gene activities indicates that the family of ZAT gene of cotton evolution was under strong purifying selection. The integration of previous transcriptome data related to NaCl stress, strongly suggests the GhZAT34 and GhZAT79 may interact with salt resistance in upland cotton. The expression level of certain ZAT genes, higher seed germination rate of transgenic Arabidopsis and gene- silenced cotton revealed that both genes were involved in the salt tolerance of upland cotton. This study may pave the substantial understandings into the role of ZATs genes in plants as well as suggest appropriate candidate genes for breeding of cotton varieties against salinity tolerance.

Comprehensive identification and expression analysis of B-Box genes in cotton

BACKGROUND

B-BOX (BBX) proteins are zinc-finger transcription factors with one or two BBX domains and sometimes a CCT domain. These proteins play an essential role in regulating plant growth and development, as well as in resisting abiotic stress. So far, the BBX gene family has been widely studied in other crops. However, no one has systematically studied the BBX gene in cotton.

RESULTS

In the present study, 17, 18, 37 and 33 BBX genes were detected in Gossypium arboreum, G. raimondii, G. hirsutum and G. barbadense, respectively, via genome-wide identification. Phylogenetic analysis showed that all BBX genes were divided into 5 main categories. The protein motifs and exon/intron structures showed that each group of BBX genes was highly conserved. Collinearity analysis revealed that the amplification of BBX gene family in Gossypium spp. was mainly through segmental replication. Nonsynonymous (Ka)/ synonymous (Ks) substitution ratios indicated that the BBX gene family had undergone purification selection throughout the long-term natural selection process. Moreover, transcriptomic data showed that some GhBBX genes were highly expressed in floral organs. The qRT-PCR results showed that there were significant differences in GhBBX genes in leaves and shoot apexes between early-maturing materials and late-maturing materials at most periods. Yeast two-hybrid results showed that GhBBX5/GhBBX23 and GhBBX8/GhBBX26 might interact with GhFT. Transcriptome data analysis and qRT-PCR verification showed that different GhBBX genes had different biological functions in abiotic stress and phytohormone response.

CONCLUSIONS

Our comprehensive analysis of BBX in G. hirsutum provided a basis for further study on the molecular role of GhBBXs in regulating flowering and cotton resistance to abiotic stress.