Promoter variations of ClERF1 gene determines flesh firmness in watermelon.

BACKGROUND: Flesh firmness is a critical factor that influences fruit storability, shelf-life and consumer's preference as well. However, less is known about the key genetic factors that are associated with flesh firmness in fresh fruits like watermelon. RESULTS: In this study, through bulk segregant analysis (BSA-seq), we identified a quantitative trait locus (QTL) that influenced variations in flesh firmness among recombinant inbred lines (RIL) developed from cross between the Citrullus mucosospermus accession ZJU152 with hard-flesh and Citrullus lanatus accession ZJU163 with soft-flesh. Fine mapping and sequence variations analyses revealed that ethylene-responsive factor 1 (ClERF1) was the most likely candidate gene for watermelon flesh firmness. Furthermore, several variations existed in the promoter region between ClERF1 of two parents, and significantly higher expressions of ClERF1 were found in hard-flesh ZJU152 compared with soft-flesh ZJU163 at key developmental stages. DUAL-LUC and GUS assays suggested much stronger promoter activity in ZJU152 over ZJU163. In addition, the kompetitive allele-specific PCR (KASP) genotyping datasets of RIL populations and germplasm accessions further supported ClERF1 as a possible candidate gene for fruit flesh firmness variability and the hard-flesh genotype might only exist in wild species C. mucosospermus. Through yeast one-hybrid (Y1H) and dual luciferase assay, we found that ClERF1 could directly bind to the promoters of auxin-responsive protein (ClAux/IAA) and exostosin family protein (ClEXT) and positively regulated their expressions influencing fruit ripening and cell wall biosynthesis. CONCLUSIONS: Our results indicate that ClERF1 encoding an ethylene-responsive factor 1 is associated with flesh firmness in watermelon and provide mechanistic insight into the regulation of flesh firmness, and the ClERF1 gene is potentially applicable to the molecular improvement of fruit-flesh firmness by design breeding.

Editing of ORF138 restores fertility of Ogura cytoplasmic male sterile broccoli via mitoTALENs.

Cytoplasmic male sterility (CMS), encoded by the mitochondrial open reading frames (ORFs), has long been used to economically produce crop hybrids. However, the utilization of CMS also hinders the exploitation of sterility and fertility variation in the absence of a restorer line, which in turn narrows the genetic background and reduces biodiversity. Here, we used a mitochondrial targeted transcription activator-like effector nuclease (mitoTALENs) to knock out ORF138 from the Ogura CMS broccoli hybrid. The knockout was confirmed by the amplification and re-sequencing read mapping to the mitochondrial genome. As a result, knockout of ORF138 restored the fertility of the CMS hybrid, and simultaneously manifested a cold-sensitive male sterility. ORF138 depletion is stably inherited to the next generation, allowing for direct use in the breeding process. In addition, we proposed a highly reliable and cost-effective toolkit to accelerate the life cycle of fertile lines from CMS-derived broccoli hybrids. By applying the k-mean clustering and interaction network analysis, we identified the central gene networks involved in the fertility restoration and cold-sensitive male sterility. Our study enables mitochondrial genome editing via mitoTALENs in Brassicaceae vegetable crops and provides evidence that the sex production machinery and its temperature-responsive ability are regulated by the mitochondria.

The coiled-coil protein gene WPRb confers recessive resistance to Cucumber green mottle mosaic virus.

Cucumber green mottle mosaic virus (CGMMV) is one of the major global quarantine viruses and causes severe symptoms in Cucurbit crops, particularly with regard to fruit decay. However, the genetic mechanisms that control plant resistance to CGMMV have yet to be elucidated. Here, we found that WPRb, a weak chloroplast movement under blue light 1 and plastid movement impaired 2-related protein family gene, is recessively associated with CGMMV resistance in watermelon (Citrullus lanatus). We developed a reproducible marker based on a single non-synonymous substitution (G1282A) in WPRb, which can be used for marker-assisted selection for CGMMV resistance in watermelon. Editing of WPRb conferred greater tolerance to CGMMV. We found WPRb targets to the plasmodesmata (PD) and biochemically interacts with the CGMMV movement protein, facilitating viral intercellular movement by affecting the permeability of PD. Our findings enable us to genetically control CGMMV resistance in planta by using precise genome editing techniques targeted to WPRb.

Pan-genome analysis sheds light on structural variation-based dissection of agronomic traits in melon crops.

Sweetness and appearance of fresh fruits are key palatable and preference attributes for consumers and are often controlled by multiple genes. However, fine-mapping the key loci or genes of interest by single genome-based genetic analysis is challenging. Herein, we present the chromosome-level genome assembly of 1 landrace melon accession (Cucumis melo ssp. agrestis) with wild morphologic features and thus construct a melon pan-genome atlas via integrating sequenced melon genome datasets. Our comparative genomic analysis reveals a total of 3.4 million genetic variations, of which the presence/absence variations (PAVs) are mainly involved in regulating the function of genes for sucrose metabolism during melon domestication and improvement. We further resolved several loci that are accountable for sucrose contents, flesh color, rind stripe, and suture using a structural variation (SV)-based genome-wide association study. Furthermore, via bulked segregation analysis (BSA)-seq and map-based cloning, we uncovered that a single gene, (CmPIRL6), determines the edible or inedible characteristics of melon fruit exocarp. These findings provide important melon pan-genome information and provide a powerful toolkit for future pan-genome-informed cultivar breeding of melon.

A large presence/absence variation in the promotor of the ClLOG gene determines trichome elongation in watermelon.

KEY MESSAGE: The ClLOG gene encoding a cytokinin riboside 5'-monophosphate phosphoribohydrolase determines trichome length in watermelon, which is associated with its promoter variations. Trichomes, which are differentiated from epidermal cells, are special accessory structures that cover the above-ground organs of plants and possibly contribute to biotic and abiotic stress resistance. Here, a bulked segregant analysis (BSA) of an F2 population with significant variations in trichome length was undertaken. A 1.84-Mb candidate region on chromosome 10 was associated with trichome length. Resequencing and fine-mapping analyses indicated that a 12-kb structural variation in the promoter of Cla97C10G203450 (ClLOG) led to a significant expression difference in this gene in watermelon lines with different trichome lengths. In addition, a virus-induced gene silencing analysis confirmed that ClLOG positively regulated trichome elongation. These findings provide new information and identify a potential target gene for controlling multicellular trichome elongation in watermelon.

Structural variation of GL1 gene determines the trichome formation in Brassica juncea.

KEY MESSAGE: A 448 kb region on chromosome B02 was delimited to be associated with trichome trait in Brassica juncea, in which the BjuVB02G54610 gene with a structural variation of 3 kb structure variation (SV) encoding a MYB transcription factor was predicted as the possible candidate gene. Mustards (Brassica juncea) are allopolyploid crops in the worldwide, and trichomes are essential quality attributes that significantly influence its taste and palpability in vegetable-use cultivars. As important accessory tissues from specialized epidermal cells, trichomes also play an important role in mitigating biotic and abiotic stresses. In this study, we constructed a F2 segregating population using YJ27 with intensive trichome leaves and 03B0307 with glabrous leaves as parents. By bulked segregant analysis (BSA-seq), we obtained a 2.1 Mb candidate region on B02 chromosome associated with the trichome or glabrous trait formation. Then, we used 13 Kompetitive Allele Specific PCR (KASP) markers for fine mapping and finally narrowed down the candidate region to about 448 kb in length. Interestingly, among the region, there was a 3 kb sequence deletion that located on the BjuVB02G54610 gene in the F2 individuals with trichome leaves. Genotyping results of F2 populations confirmed this deletion (R2 = 81.44%) as a major QTL. Natural population re-sequencing analysis and genotyping results further validated the key role of the 3 kb structure variation (SV) of insertion/deletion type in trichome development in B. juncea. Our findings provide important information on the formation of trichomes and potential target gene for breeding vegetable mustards.

Allelic variations of ClACO gene improve nitrogen uptake via ethylene-mediated root architecture in watermelon.

KEY MESSAGE: The ClACO gene encoding 1-aminocyclopropane-1-carboxylate oxidase enabled highly efficient 15N uptake in watermelon. Nitrogen is one of the most essential nutrient elements that play a pivotal role in regulating plant growth and development for crop productivity. Elucidating the genetic basis of high nitrogen uptake is the key to improve nitrogen use efficiency for sustainable agricultural productivity. Whereas previous researches on nitrogen absorption process are mainly focused on a few model plants or crops. To date, the causal genes that determine the efficient nitrogen uptake of watermelon have not been mapped and remains largely unknown. Here, we fine-mapped the 1-aminocyclopropane-1-carboxylate oxidase (ClACO) gene associated with nitrogen uptake efficiency in watermelon via bulked segregant analysis (BSA). The variations in the ClACO gene led to the changes of gene expression levels between two watermelon accessions with different nitrogen uptake efficiencies. Intriguingly, in terms of the transcript abundance of ClACO, it was concomitant with significant differences in ethylene evolutions in roots and root architectures between the two accessions and among the different genotypic offsprings of the recombinant BC2F1(ZJU132)-18. These findings suggest that ethylene as a negative regulator altered nitrogen uptake efficiency in watermelon by controlling root development. In conclusion, our current study will provide valuable target gene for precise breeding of 'green' watermelon varieties with high-nitrogen uptake efficiencies.

Design, synthesis and biological evaluation of novel N-(methyl-d3) pyridazine-3-carboxamide derivatives as TYK2 inhibitors.

As a mediator of pro-inflammatory cytokines, TYK2 is an attractive target to treat autoimmunity diseases. Herein, we reported the design, synthesis, and structure-activity relationships (SARs) of N-(methyl-d3) pyridazine-3-carboxamide derivatives as TYK2 inhibitors. Among them, compound 24 exhibited acceptable inhibition activity against STAT3 phosphorylation. Furthermore, 24 showed satisfactory selectivities toward other members of JAK family and performed a good stability profile in liver microsomal assay. Pharmacokinetics (PK) study indicated that compound 24 has reasonable PK exposures. In anti-CD40-induced colitis models, compound 24 was orally highly effective with no significant hERG and CYP isozymes inhibition. These results indicated that compound 24 was worthy of further investigation for the development of anti-autoimmunity diseases agents.

Integrated Bulk Segregant Analysis, Fine Mapping, and Transcriptome Revealed QTLs and Candidate Genes Associated with Drought Adaptation in Wild Watermelon.

Drought stress has detrimental effects on crop productivity worldwide. A strong root system is crucial for maintaining water and nutrients uptake under drought stress. Wild watermelons possess resilient roots with excellent drought adaptability. However, the genetic factors controlling this trait remain uninvestigated. In this study, we conducted a bulk segregant analysis (BSA) on an F2 population consisting of two watermelon genotypes, wild and domesticated, which differ in their lateral root development under drought conditions. We identified two quantitative trait loci (qNLR_Dr. Chr01 and qNLR_Dr. Chr02) associated with the lateral root response to drought. Furthermore, we determined that a small region (0.93 Mb in qNLR_Dr. Chr01) is closely linked to drought adaptation through quantitative trait loci (QTL) validation and fine mapping. Transcriptome analysis of the parent roots under drought stress revealed unique effects on numerous genes in the sensitive genotype but not in the tolerant genotype. By integrating BSA, fine mapping, and the transcriptome, we identified six genes, namely L-Ascorbate Oxidase (AO), Cellulose Synthase-Interactive Protein 1 (CSI1), Late Embryogenesis Abundant Protein (LEA), Zinc-Finger Homeodomain Protein 2 (ZHD2), Pericycle Factor Type-A 5 (PFA5), and bZIP transcription factor 53-like (bZIP53-like), that might be involved in the drought adaptation. Our findings provide valuable QTLs and genes for marker-assisted selection in improving water-use efficiency and drought tolerance in watermelon. They also lay the groundwork for the genetic manipulation of drought-adapting genes in watermelon and other Cucurbitacea species.

An allelic variant in the ACS7 gene promotes primary root growth in watermelon.

KEY MESSAGE: Gene mining in a C. lanatus × C. amarus population revealed one gene, ACS7, linked to primary root elongation in watermelon. Watermelon is a xerophytic crop characterized by a long primary root and robust lateral roots. Therefore, watermelon serves as an excellent model for studying root elongation and development. However, the genetic mechanism underlying the primary root elongation in watermelon remains unknown. Herein, through bulk segregant analysis we identified a genetic locus, qPRL.Chr03, controlling primary root length (PRL) using two different watermelon species (Citrullus lanatus and Citrullus amarus) that differ in their root architecture. Fine mapping revealed that xaa-Pro dipeptidase and 1-aminocyclopropane-1-carboxylate synthase 7 (ACS7) are candidate regulators of the primary root growth. Allelic variation in the delimited region among 193 watermelon accessions indicated that the long-root alleles might only exist in C. amarus. Interestingly, the discrepancy in PRL among the C. amarus accessions was clearly associated with a nonsynonymous single nucleotide polymorphism variant within the ACS7 gene. The ACS7 expression and ethylene levels in the primary root tips suggested that ethylene is a negative regulator of root elongation in watermelon, as supported by the application of 1-aminocyclopropane-1-carboxylate (ACC, the ethylene precursor) or 2-aminoethoxyvinyl glycine (AVG, an ACS inhibitor). To the best of our knowledge, these findings provide the first description of the genetic basis of root elongation in watermelon. The detected markers of the ACS7 gene will facilitate marker-assisted selection for the PRL trait to improve water and nutrient use efficacy in watermelon and beyond.

The casein kinase 2 ß subunit CK2B1 is required for swollen stem formation via cell cycle control in vegetable Brassica juncea.

The swollen stem is a determinant of yield for the stem-type vegetable Brassica juncea that is representative of vegetative organ formation. However, the genetic mechanism underlying swollen stem formation and its regulation remains unknown. In this study, we identified a casein kinase 2 ß subunit 1 (CK2B1) and revealed its role in swollen stem formation. Genotyping analysis revealed that a homozygous variation in the CK2B1 promoter is responsible for swollen stem formation, and the promoter activity of CK2B1 was significantly associated with the variations between swollen stem and non-swollen stem types. CK2B1 was exclusively located in the nucleus and expressed in the stem nodes of the plant. Swollen stem formation was blocked when CK2B1 expression was silenced, and induced in a backcross population carrying a swollen stem genotype, which indicates that CK2B1 is required for swollen stem formation. Cell numbers were increased during swollen stem formation and decreased in CK2B1-silenced expression plant, indicating that CK2B1 regulates swollen stem formation via cell division. CK2B1 directly interacted with E2Fa, a regulator of G1/S transition in the cell cycle, in which CK2 phosphorylates E2Fa. Our results revealed that CK2B1 affects swollen stem formation via the control of the cell cycle. These findings help to elucidate the signals that control swollen stem formation and provide a promising molecular target to enhance the yield of vegetative organ formation.

Genomic signatures of vegetable and oilseed allopolyploid Brassica juncea and genetic loci controlling the accumulation of glucosinolates.

Allopolyploid Brassica juncea crops in Brassicaceae are becoming increasingly revitalized as vegetables and oilseeds owing to wide adaptability and significant economic values. However, the genomic differentiation of diversified vegetables and oilseed B. juncea and the genetic basis underlying glucosinolates accumulation have yet to be elucidated. To address this knowledge gap, we report the sequencing of pairwise genomes of vegetable and oilseed B. juncea at chromosome scale. Comparative genomics analysis unveils panoramic structural variation footprints, particularly the genetic loci of HSP20 and TGA1 associated with abiotic and biotic stresses responses between oilseed and vegetable subgroups. We anchored two major loci of MYB28 (HAG1) orthologues caused by copy number variations on A02 and A09 chromosomes using scored genomic SNPs-based GWAS that are responsible for seed oil quality-determining glucosinolates biosynthesis. These findings will provide valuable repertories of polyploidy genomic information enabling polyploidy genome evolution studies and precise genomic selections for crucial traits like functional components of glucosinolates in B. juncea crops and beyond.

MutS HOMOLOG1 mediates fertility reversion from cytoplasmic male sterile Brassica juncea in response to environment.

Spontaneous fertility reversion has been documented in cytoplasmic male sterile (CMS) plants of several species, influenced in frequency by nuclear genetic background. In this study, we found that MutS HOMOLOG1 (MSH1) mediates fertility reversion via substoichiometric shifting (SSS) of the CMS-associated mitochondrial Open Reading Frame 220 (ORF220), a process that may be regulated by pollination signalling in Brassica juncea. We show that plants adjust their growth and development in response to unsuccessful pollination. Measurable decrease in MSH1 transcript levels and evidence of ORF220 SSS under non-pollination conditions suggest that this nuclear-mitochondrial interplay influences fertility reversion in CMS plants in response to physiological signals. Suppression of MSH1 expression induced higher frequency SSS in CMS plants than occurs normally. Transcriptional analysis of floral buds under pollination and non-pollination conditions, and the response of MSH1 expression to different sugars, supports the hypothesis that carbon flux is involved in the pollination signalling of fertility reversion in CMS plants. Our findings suggest that facultative gynodioecy as a reproductive strategy may incorporate environmentally responsive genes like MSH1 as an "on-off" switch for sterility-fertility transition under ecological conditions of reproductive isolation.

Investigation of the relationship between heart rate and functional class in pulmonary hypertension.

The utility of a non-linear mixed effects model to model heart rate is examined. The heart rate acceleration is derived as a parameter from this model. The relationship between different potential measures of disease severity including heart rate acceleration is examined. Our study is focused on heart rate variability (HRV), heart rate acceleration (HRA), oxygen saturation (SaO2) and the six-minute walk distance (6MWD) as well as their relationship to WHO functional class. The results and conclusions are derived from data were collected by the Children Hospital of Colorado.

Ethylene-responsive factor 4 is associated with the desirable rind hardness trait conferring cracking resistance in fresh fruits of watermelon.

Fruit rind plays a pivotal role in alleviating water loss and disease and particularly in cracking resistance as well as the transportability, storability and shelf-life quality of the fruit. High susceptibility to cracking due to low rind hardness is largely responsible for severe annual yield losses of fresh fruits such as watermelon in the field and during the postharvest process. However, the candidate gene controlling the rind hardness phenotype remains unclear to date. Herein, we report, for the first time, an ethylene-responsive transcription factor 4 (ClERF4) associated with variation in rind hardness via a combinatory genetic map with bulk segregant analysis (BSA). Strikingly, our fine-mapping approach revealed an InDel of 11 bp and a neighbouring SNP in the ClERF4 gene on chromosome 10, conferring cracking resistance in F2 populations with variable rind hardness. Furthermore, the concomitant kompetitive/competitive allele-specific PCR (KASP) genotyping data sets of 104 germplasm accessions strongly supported candidate ClERF4 as a causative gene associated with fruit rind hardness variability. In conclusion, our results provide new insight into the underlying mechanism controlling rind hardness, a desirable trait in fresh fruit. Moreover, the findings will further enable the molecular improvement of fruit cracking resistance in watermelon via precisely targeting the causative gene relevant to rind hardness, ClERF4.

AMPKα1 overexpression improves postoperative cognitive dysfunction in aged rats through AMPK-Sirt1 and autophagy signaling.

Postoperative cognitive dysfunction (POCD) is a common complication in elderly patients who undergo surgery involving anesthesia. Its underlying mechanisms remain unclear. Autophagy plays an important role in the damage and repair of the nervous system and is associated with the development of POCD. Using a rat model, adenosine monophosphate-activated protein kinase α1 (AMPKα1), an important autophagy regulator, was found to be significantly downregulated in rats with POCD that was induced by sevoflurane anesthesia or by appendectomy. Overexpression of AMPKα1-ameliorated POCD, as indicated by decreased escape latencies and increased target quadrant swimming times, swimming distances, and platform crossing times during Morris water maze tests. AMPKα1 overexpression activated autophagy signals by increasing the expression of light chain 3 II (LC3-II) and Beclin1 and decreasing the expression of p62 in the hippocampus of rats with POCD. Moreover, blocking autophagy by 3-methyladenine partly attenuated AMPKα1-mediated POCD improvement. Furthermore, overexpression of AMPKα1 could upregulate the expression of p-AMPK and Sirt1 in the hippocampus of rats with POCD. Intriguingly, inhibiting AMPK signals via Compound C effectively attenuated AMPKα1-mediated POCD improvement, concomitant with the downregulation of p-AMPK, Sirt1, LC3-II, and Beclin1 and the upregulation of p62. We thus concluded that overexpression of AMPKα1 can improve POCD via the AMPK-Sirt1 and autophagy signaling pathway.

Phytochrome A signal transduction 1 and CONSTANS-LIKE 13 coordinately orchestrate shoot branching and flowering in leafy Brassica juncea.

Branching is a major determinant of crop yield, and enables vigorous shoot growth and the production of a dense canopy. Phytochrome A signal transduction 1 (PAT1) positively regulates phytochrome A signal transduction in response to light, but its effects on branching remain unknown. In this study, we mapped PAT1, and revealed a previously unknown role related to branching and flowering in leafy Brassica juncea. Earlier and increased branching was observed when PAT1 expression was down-regulated, implying that PAT1 negatively regulates shoot branching. Additionally, down-regulated PAT1 expression reversed the inhibited branching induced by far-red light, suggesting PAT1 is involved in the shade avoidance response. PAT1 negatively regulated branching only after bud initiation. The observed interaction between PAT1 and BRC1 implied that PAT1 influences bud outgrowth in a BRC1-dependent manner. Biochemical and genetic evidence indicate that PAT1 directly interacts with CONSTANS-LIKE 13 (COL13), which negatively regulates flowering, with the resulting PAT1-COL13 complex mediating shoot branching and flowering. Our findings reveal a new crosstalk modality between phytochrome signalling and flowering pathways during the regulation of shoot branching and flowering. The data presented herein may be useful for future studies involving the editing of the GRAS family transcription factor PAT1 gene to enhance crop productivity and enable earlier harvesting.

Characterization of watermelon anther and its programmed cell death-associated events during dehiscence under cold stress.

KEY MESSAGE: The 'neglected' thermophile fruit crop of watermelon was first used as a model crop to study the PCD associated with anther dehiscence in cold-exposed condition during anther development. Anther dehiscence ensures normal pollen release and successful fertilization at fruit-setting stages in flowering plants. However, most researches pertinent to anther dehiscence are centered on model plant and/or major field crops under optimal growth condition. Due to anther indehiscence in cold condition, crop plants of thermophile tropical or subtropical fruit crops fail to accomplish timely pollination and fertilization, resulting in a great yield loss annually. Herein, we developed an ideal model crop for studying the programmed cell death (PCD) associated with anther dehiscence under low-temperature stress using the S-shaped spiral anther in watermelon as instead. Our results revealed that, including the tapetal cell layers, both cells of the interlocular septum and the stomium were blocked in PCD associated with anther dehiscence at 15 °C. Likewise, TUNEL assays visualized the evidence that low temperature at 15 °C interferes with not only the PCD of tapetal cells, but also the PCD of interlocular septum and stomium. Furthermore, the expressions of genes correlated with PCD of tapetum and stomium were significantly inhibited at 15 °C, suggesting that low temperature affects anther dehiscence by inhibiting PCD of sporophytic tissue-related gene expressions. The findings of the current research provide mechanistic insights into anther indehiscence leading to poor fruit-setting for thermophile fruit crop such as watermelon under adverse cold condition in flowering.

Eukaryotic translation initiation factor 2B-beta (eIF2Bß), a new class of plant virus resistance gene.

Recessive resistances to plant viruses in the Potyvirus genus have been found to be based on mutations in the plant eukaryotic translation initiation factors, eIF4E and eIF4G or their isoforms. Here we report that natural, monogenic recessive resistance to the Potyvirus Turnip mosaic virus (TuMV) has been found in a number of mustard (Brassica juncea) accessions. Bulked segregant analysis and sequencing of resistant and susceptible plant lines indicated the resistance is controlled by a single recessive gene, recessive TuMV resistance 03 (retr03), an allele of the eukaryotic translation initiation factor 2B-beta (eIF2Bß). Silencing of eIF2Bß in a TuMV-susceptible mustard plant line and expression of eIF2Bß from a TuMV-susceptible line in a TuMV-resistant mustard plant line confirmed the new resistance mechanism. A functional copy of a specific allele of eIF2Bß is required for efficient TuMV infection. eIF2Bß represents a new class of virus resistance gene conferring resistance to any pathogen. eIF2B acts as a guanine nucleotide exchange factor (GEF) for its GTP-binding protein partner eIF2 via interaction with eIF2·GTP at an early step in translation initiation. Further genotyping indicated that a single non-synonymous substitution (A120G) in the N-terminal region of eIF2Bß was responsible for the TuMV resistance. A reproducible marker has been developed, facilitating marker-assisted selection for TuMV resistance in B. juncea. Our findings provide a new target for seeking natural resistance to potyviruses and new opportunities for the control of potyviruses using genome editing techniques targeted on eIF2Bß.

Genome-wide identification and expression analysis of the ClTCP transcription factors in Citrullus lanatus.

BACKGROUND: The plant-specific TCP transcription factor family, which is involved in the regulation of cell growth and proliferation, performs diverse functions in multiple aspects of plant growth and development. However, no comprehensive analysis of the TCP family in watermelon (Citrullus lanatus) has been undertaken previously. RESULTS: A total of 27 watermelon TCP encoding genes distributed on nine chromosomes were identified. Phylogenetic analysis clustered the genes into 11 distinct subgroups. Furthermore, phylogenetic and structural analyses distinguished two homology classes within the ClTCP family, designated Class I and Class II. The Class II genes were differentiated into two subclasses, the CIN subclass and the CYC/TB1 subclass. The expression patterns of all members were determined by semi-quantitative PCR. The functions of two ClTCP genes, ClTCP14a and ClTCP15, in regulating plant height were confirmed by ectopic expression in Arabidopsis wild-type and ortholog mutants. CONCLUSIONS: This study represents the first genome-wide analysis of the watermelon TCP gene family, which provides valuable information for understanding the classification and functions of the TCP genes in watermelon.