MADS-box genes underground becoming mainstream: plant root developmental mechanisms

Martínez-Castilla L, García-Sandoval R, Ballester P, Ferrándiz C, Sanchez MDLP, García-Ponce B, Garay-Arroyo A, R. Álvarez-Buylla E. HDACs MADS-domain protein interaction: a case study of HDA15 and XAL1 in Arabidopsis thaliana

Cellular behavior, cell differentiation and ontogenetic development in eukaryotes result from complex interactions between epigenetic and classic molecular genetic mechanisms, with many of these interactions still to be elucidated. Histone deacetylase enzymes (HDACs) promote the interaction of histones with DNA by compacting the nucleosome, thus causing transcriptional repression. MADS-domain transcription factors are highly conserved in eukaryotes and participate in controlling diverse developmental processes in animals and plants, as well as regulating stress responses in plants. In this work, we focused on finding out putative interactions of Arabidopsis thaliana HDACs and MADS-domain proteins using an evolutionary perspective combined with bioinformatics analyses and testing the more promising predicted interactions through classic molecular biology tools. Through bioinformatic analyses, we found similarities between HDACs proteins from different organisms, which allowed us to predict a putative protein-protein interaction between the Arabidopsis thaliana deacetylase HDA15 and the MADS-domain protein XAANTAL1 (XAL1). The results of two-hybrid and Bimolecular Fluorescence Complementation analysis demonstrated in vitro and in vivo HDA15-XAL1 interaction in the nucleus. Likely, this interaction might regulate developmental processes in plants as is the case for this type of interaction in animals.

An Overview on MADS Box Members in Plants: A Meta-Review

Most of the studied MADS box members are linked to flowering and fruit traits. However, higher volumes of studies on type II of the two types so far suggest that the florigenic effect of the gene members could just be the tip of the iceberg. In the current study, we used a systematic approach to obtain a general overview of the MADS box members' cross-trait and multifactor associations, and their pleiotropic potentials, based on a manually curated local reference database. While doing so, we screened for the co-occurrence of terms of interest within the title or abstract of each reference, with a threshold of three hits. The analysis results showed that our approach can retrieve multi-faceted information on the subject of study (MADS box gene members in the current case), which could otherwise have been skewed depending on the authors' expertise and/or volume of the literature reference base. Overall, our study discusses the roles of MADS box members in association with plant organs and trait-linked factors among plant species. Our assessment showed that plants with most of the MADS box member studies included tomato, apple, and rice after Arabidopsis. Furthermore, based on the degree of their multi-trait associations, FLC, SVP, and SOC1 are suggested to have relatively higher pleiotropic potential among others in plant growth, development, and flowering processes. The approach devised in this study is expected to be applicable for a basic understanding of any study subject of interest, regardless of the depth of prior knowledge.

OsMADS6-OsMADS32 and REP1 control palea cellular heterogeneity and morphogenesis in rice

Precise regulation of cell proliferation and differentiation is vital for organ morphology. Rice palea, serving as sepal, comprises two distinct regions: the marginal region (MRP) and body of palea (BOP), housing heterogeneous cell populations, which makes it an ideal system for studying organ morphogenesis. We report that the transcription factor (TF) REP1 promotes epidermal cell proliferation and differentiation in the BOP, resulting in hard silicified protrusion cells, by regulating the cyclin-dependent kinase gene, OsCDKB1;1. Conversely, TFs OsMADS6 and OsMADS32 are expressed exclusively in the MRP, where they limit cell division rates by inhibiting OsCDKB2;1 expression and promote endoreduplication, yielding elongated epidermal cells. Furthermore, reciprocal inhibition between the OsMADS6-OsMADS32 complex and REP1 fine-tunes the balance between cell division and differentiation during palea morphogenesis. We further show the functional conservation of these organ identity genes in heterogeneous cell growth in Arabidopsis, emphasizing a critical framework for controlling cellular heterogeneity in organ morphogenesis.

Genome-Wide Analysis of MADS-Box Gene Family Reveals CjSTK as a Key Regulator of Seed Abortion in Camellia japonica

The plant MADS-box transcription factor family is a major regulator of plant flower development and reproduction, and the AGAMOUS-LIKE11/SEEDSTICK (AGL11/STK) subfamily plays conserved functions in the seed development of flowering plants. Camellia japonica is a world-famous ornamental flower, and its seed kernels are rich in highly valuable fatty acids. Seed abortion has been found to be common in C. japonica, but little is known about how it is regulated during seed development. In this study, we performed a genome-wide analysis of the MADS-box gene the in C. japonica genome and identified 126 MADS-box genes. Through gene expression profiling in various tissue types, we revealed the C/D-class MADS-box genes were preferentially expressed in seed-related tissues. We identified the AGL11/STK-like gene, CjSTK, and showed that it contained a typical STK motif and exclusively expressed during seed development. We found a significant increase in the CjSTK expression level in aborted seeds compared with normally developing seeds. Furthermore, overexpression of CjSTK in Arabidopsis thaliana caused shorter pods and smaller seeds. Taken together, we concluded that the fine regulation of the CjSTK expression at different stages of seed development is critical for ovule formation and seed abortion in C. japonica. The present study provides evidence revealing the regulation of seed development in Camellia.

Evolutionary analysis of MADS-box genes in buckwheat species and functional study of FdMADS28 in flavonoid metabolism

The MADS-box gene family is a transcription factor family that is widely expressed in plants. It controls secondary metabolic processes in plants and encourages the development of tissues like roots and flowers. However, the phylogenetic analysis and evolutionary model of MADS-box genes in Fagopyrum species has not been reported yet. This study identified the MADS-box genes of three buckwheat species at the whole genome level, and conducted systematic evolution and physicochemical analysis. The results showed that these genes can be divided into four subfamilies, with fragment duplication being the main way for the gene family expansion. During the domestication process from golden buckwheat to tartary buckwheat and the common buckwheat, the Ka/Ks ratio indicated that most members of the family experienced strong purification selection pressure, and with individual gene pairs experiencing positive selection. In addition, we combined the expression profile data of the MADS genes, mGWAS data, and WGCNA data to mine genes FdMADS28/48/50 that may be related to flavonoid metabolism. The results also showed that overexpression of FdMADS28 could increase rutin content by decreasing Kaempferol pathway content in hairy roots, and increase the resistance and growth of hairy roots to PEG and NaCl. This study systematically analyzed the evolutionary relationship of MADS-box genes in the buckwheat species, and elaborated on the expression patterns of MADS genes in different tissues under biotic and abiotic stresses, laying an important theoretical foundation for further elucidating their role in flavonoid metabolism.

Adventitious rooting in response to long-term cold: a possible mechanism of clonal growth in alpine perennials

Arctic alpine species experience extended periods of cold and unpredictable conditions during flowering. Thus, often, alpine plants use both sexual and asexual means of reproduction to maximize fitness and ensure reproductive success. We used the arctic alpine perennial Arabis alpina to explore the role of prolonged cold exposure on adventitious rooting. We exposed plants to 4°C for different durations and scored the presence of adventitious roots on the main stem and axillary branches. Our physiological studies demonstrated the presence of adventitious roots after 21 weeks at 4°C saturating the effect of cold on this process. Notably, adventitious roots on the main stem developing in specific internodes allowed us to identify the gene regulatory network involved in the formation of adventitious roots in cold using transcriptomics. These data and histological studies indicated that adventitious roots in A. alpina stems initiate during cold exposure and emerge after plants experience growth promoting conditions. While the initiation of adventitious root was not associated with changes of DR5 auxin response and free endogenous auxin level in the stems, the emergence of the adventitious root primordia was. Using the transcriptomic data, we discerned the sequential hormone responses occurring in various stages of adventitious root formation and identified supplementary pathways putatively involved in adventitious root emergence, such as glucosinolate metabolism. Together, our results highlight the role of low temperature during clonal growth in alpine plants and provide insights on the molecular mechanisms involved at distinct stages of adventitious rooting.

Genome-wide analysis of MADS-box transcription factor gene family in wild emmer wheat (Triticum turgidum subsp. dicoccoides)

The members of MADS-box gene family have important roles in regulating the growth and development of plants. MADS-box genes are highly regarded for their potential to enhance grain yield and quality under shifting global conditions. Wild emmer wheat (Triticum turgidum subsp. dicoccoides) is a progenitor of common wheat and harbors valuable traits for wheat improvement. Here, a total of 117 MADS-box genes were identified in the wild emmer wheat genome and classified to 90 MIKCC, 3 MIKC*, and 24 M-type. Furthermore, a phylogenetic analysis and expression profiling of the emmer wheat MADS-box gene family was presented. Although some MADS-box genes belonging to SOC1, SEP1, AGL17, and FLC groups have been expanded in wild emmer wheat, the number of MIKC-type MADS-box genes per subgenome is similar to that of rice and Arabidopsis. On the other hand, M-type genes of wild emmer wheat is less frequent than that of Arabidopsis. Gene expression patterns over different tissues and developmental stages agreed with the subfamily classification of MADS-box genes and was similar to common wheat and rice, indicating their conserved functionality. Some TdMADS-box genes are also differentially expressed under drought stress. The promoter region of each of the TdMADS-box genes harbored 6 to 48 responsive elements, mainly related to light, however hormone, drought, and low-temperature related cis-acting elements were also present. In conclusion, the results provide detailed information about the MADS-box genes of wild emmer wheat. The present work could be useful in the functional genomics efforts toward breeding for agronomically important traits in T. dicoccoides.

Unregulated GmAGL82 due to Phosphorus Deficiency Positively Regulates Root Nodule Growth in Soybean

Nitrogen fixation, occurring through the symbiotic relationship between legumes and rhizobia in root nodules, is crucial in sustainable agriculture. Nodulation and soybean production are influenced by low levels of phosphorus stress. In this study, we discovered a MADS transcription factor, GmAGL82, which is preferentially expressed in nodules and displays significantly increased expression under conditions of phosphate (Pi) deficiency. The overexpression of GmAGL82 in composite transgenic plants resulted in an increased number of nodules, higher fresh weight, and enhanced soluble Pi concentration, which subsequently increased the nitrogen content, phosphorus content, and overall growth of soybean plants. Additionally, transcriptome analysis revealed that the overexpression of GmAGL82 significantly upregulated the expression of genes associated with nodule growth, such as GmENOD100, GmHSP17.1, GmHSP17.9, GmSPX5, and GmPIN9d. Based on these findings, we concluded that GmAGL82 likely participates in the phosphorus signaling pathway and positively regulates nodulation in soybeans. The findings of this research may lay the theoretical groundwork for further studies and candidate gene resources for the genetic improvement of nutrient-efficient soybean varieties in acidic soils.

Transcriptional regulation of tomato fruit ripening

An intrinsic and genetically determined ripening program of tomato fruits often depends upon the appropriate activation of tissue- and stage-specific transcription factors in space and time. The past two decades have yielded considerable progress in detailing these complex transcriptional as well as hormonal regulatory circuits paramount to fleshy fruit ripening. This non-linear ripening process is strongly controlled by the MADS-box and NOR family of proteins, triggering a transcriptional response associated with the progression of fruit ripening. Deepening insights into the connection between MADS-RIN and plant hormones related transcription factors, such as ERFs and ARFs, further conjugates the idea that several signaling units work in parallel to define an output fruit ripening transcriptome. Besides these TFs, the role of other families of transcription factors such as MYB, GLK, WRKY, GRAS and bHLH have also emerged as important ripening regulators. Other regulators such as EIN and EIL proteins also determine the transcriptional landscape of ripening fruits. Despite the abundant knowledge of the complex spectrum of ripening networks in the scientific domain, identifying more ripening effectors would pave the way for a better understanding of fleshy fruit ripening at the molecular level. This review provides an update on the transcriptional regulators of tomato fruit ripening.

Antagonistic MADS-box transcription factors SEEDSTICK and SEPALLATA3 form a transcriptional regulatory network that regulates seed oil accumulation

Transcriptional regulation is essential for balancing multiple metabolic pathways that influence oil accumulation in seeds. Thus far, the transcriptional regulatory mechanisms that govern seed oil accumulation remain largely unknown. Here, we identified the transcriptional regulatory network composed of MADS-box transcription factors SEEDSTICK (STK) and SEPALLATA3 (SEP3), which bridges several key genes to regulate oil accumulation in seeds. We found that STK, highly expressed in the developing embryo, positively regulates seed oil accumulation in Arabidopsis (Arabidopsis thaliana). Furthermore, we discovered that SEP3 physically interacts with STK in vivo and in vitro. Seed oil content is increased by the SEP3 mutation, while it is decreased by SEP3 overexpression. The chromatin immunoprecipitation, electrophoretic mobility shift assay, and transient dual-luciferase reporter assays showed that STK positively regulates seed oil accumulation by directly repressing the expression of MYB5, SEP3, and SEED FATTY ACID REDUCER 4 (SFAR4). Moreover, genetic and molecular analyses demonstrated that STK and SEP3 antagonistically regulate seed oil production and that SEP3 weakens the binding ability of STK to MYB5, SEP3, and SFAR4. Additionally, we demonstrated that TRANSPARENT TESTA 8 (TT8) and ACYL-ACYL CARRIER PROTEIN DESATURASE 3 (AAD3) are direct targets of MYB5 during seed oil accumulation in Arabidopsis. Together, our findings provide the transcriptional regulatory network antagonistically orchestrated by STK and SEP3, which fine tunes oil accumulation in seeds.

Ectopic Expression of MADS-Box Transcription Factor VvAGL12 from Grape Promotes Early Flowering, Plant Growth, and Production by Regulating Cell-Wall Architecture in Arabidopsis

The MADS-box family, a substantial group of plant transcription factors, crucially regulates plant growth and development. Although the functions of AGL12-like subgroups have been elucidated in Arabidopsis, rice, and walnut, their roles in grapes remain unexplored. In this study, we isolated VvAGL12, a member of the grape MADS-box group, and investigated its impact on plant growth and biomass production. VvAGL12 was found to localize in the nucleus and exhibit expression in both vegetative and reproductive organs. We introduced VvAGL12 into Arabidopsis thaliana ecotype Columbia-0 and an agl12 mutant. The resulting phenotypes in the agl12 mutant, complementary line, and overexpressed line underscored VvAGL12's ability to promote early flowering, augment plant growth, and enhance production. This was evident from the improved fresh weight, root length, plant height, and seed production, as well as the reduced flowering time. Subsequent transcriptome analysis revealed significant alterations in the expression of genes associated with cell-wall modification and flowering in the transgenic plants. In summary, the findings highlight VvAGL12's pivotal role in the regulation of flowering timing, overall plant growth, and development. This study offers valuable insights, serving as a reference for understanding the influence of the VvAGL12 gene in other plant species and addressing yield-related challenges.

Nuclear translocation of OsMADS25 facilitated by OsNAR2.1 in reponse to nitrate signals promotes rice root growth by targeting OsMADS27 and OsARF7

Nitrate is an important nitrogen source and signaling molecule that regulates plant growth and development. Although several components of the nitrate signaling pathway have been identified, the detailed mechanisms are still unclear. Our previous results showed that OsMADS25 can regulate root development in response to nitrate signals, but the mechanism is still unknown. Here, we try to answer two key questions: how does OsMADS25 move from the cytoplasm to the nucleus, and what are the direct target genes activated by OsMADS25 to regulate root growth after it moves to the nucleus in response to nitrate? Our results demonstrated that OsMADS25 moves from the cytoplasm to the nucleus in the presence of nitrate in an OsNAR2.1-dependent manner. Chromatin immunoprecipitation sequencing, chromatin immunoprecipitation qPCR, yeast one-hybrid, and luciferase experiments showed that OsMADS25 directly activates the expression of OsMADS27 and OsARF7, which are reported to be associated with root growth. Finally, OsMADS25-RNAi lines, the Osnar2.1 mutant, and OsMADS25-RNAi Osnar2.1 lines exhibited significantly reduced root growth compared with the wild type in response to nitrate supply, and expression of OsMADS27 and OsARF7 was significantly suppressed in these lines. Collectively, these results reveal a new mechanism by which OsMADS25 interacts with OsNAR2.1. This interaction is required for nuclear accumulation of OsMADS25, which promotes OsMADS27 and OsARF7 expression and root growth in a nitrate-dependent manner.

Physiological, anatomical and quality indexes of root tuber formation and development in chayote (Sechium edule)

BACKGROUND

Chayote is an underutilized species of Cucurbitaceae. It is rich in nutrients such as protein, minerals, phenols and its extracts have anti-cardiovascular and anti-cancer effects, making it a versatile plant for both medicinal and culinary purposes. Although research on its root tuber is limited, they are rich in starch and have a structure similar to that of potatoes, cassava, and sweet potatoes. Therefore, they can serve as potential substitutes for potatoes and offer promising prospects as agricultural and industrial resources. However, the physiological and cellular mechanisms of chayote root tuber formation and development are still unclear.

RESULTS

In this study, we observed the growth habit of 'Tuershao' (high yield of root tuber). The results revealed that the tuber enlargement period of 'Tuershao' lasts approximately 120 days, with the early enlargement phase occurring during 0-30 days, rapid enlargement phase during 30-90 days, and maturation phase during 90-120 days. Physiological indicators demonstrated a gradual increase in starch content as the tuber developed. The activities of sucrose synthase (SUS) and invertase (VIN) showed a consistent trend, reaching the highest level in the rapid expansion period, which was the key enzyme affecting tuber expansion. Moreover, the special petal like structure formed by the secondary phloem and secondary xylem of the tuber resulted in its enlargement, facilitating the accumulation of abundant starch within the thin-walled cells of this structure. Principal component analysis further confirmed that starch content, SUS and VIN activities, as well as the concentrations of calcium (Ca), iron (Fe), and selenium (Se), were the major factors influencing tuber development. Moreover, the low temperature environment not only promoted the growth of 'Tuershao' tubers but also enhanced the accumulation of nutritional substances.

CONCLUSIONS

These findings contribute to a deeper understanding of the formation and developmental mechanisms of 'Tuershao' tubers, providing valuable guidance for cultivation practices aimed at improving crop yield.

TM3 and STM3 Promote Flowering Together with FUL2 and MBP20, but Act Antagonistically in Inflorescence Branching in Tomato

The moment at which a plant transitions to reproductive development is paramount to its life cycle and is strictly controlled by many genes. The transcription factor SUPPRESSOR OF OVEREXPRESSION OF CONSTANS 1 (SOC1) plays a central role in this process in Arabidopsis. However, the role of SOC1 in tomato (Solanum lycopersicum) has been sparsely studied. Here, we investigated the function of four tomato SOC1 homologs in the floral transition and inflorescence development. We thoroughly characterized the SOC1-like clade throughout the Solanaceae and selected four tomato homologs that are dynamically expressed upon the floral transition. We show that of these homologs, TOMATO MADS 3 (TM3) and SISTER OF TM3 (STM3) promote the primary and sympodial transition to flowering, while MADS-BOX PROTEIN 23 (MBP23) and MBP18 hardly contribute to flowering initiation in the indeterminate cultivar Moneyberg. Protein-protein interaction assays and whole-transcriptome analysis during reproductive meristem development revealed that TM3 and STM3 interact and share many targets with FRUITFULL (FUL) homologs, including cytokinin regulators. Furthermore, we observed that mutating TM3/STM3 affects inflorescence development, but counteracts the inflorescence-branching phenotype of ful2 mbp20. Collectively, this indicates that TM3/STM3 promote the floral transition together with FUL2/MBP20, while these transcription factors have opposite functions in inflorescence development.

Genome-Wide Identification of MADS-Box Genes in Taraxacum kok-saghyz and Taraxacum mongolicum: Evolutionary Mechanisms, Conserved Functions and New Functions Related to Natural Rubber Yield Formation

MADS-box transcription regulators play important roles in plant growth and development. However, very few MADS-box genes have been isolated in the genus Taraxacum, which consists of more than 3000 species. To explore their functions in the promising natural rubber (NR)-producing plant Taraxacum kok-saghyz (TKS), MADS-box genes were identified in the genome of TKS and the related species Taraxacum mongolicum (TM; non-NR-producing) via genome-wide screening. In total, 66 TkMADSs and 59 TmMADSs were identified in the TKS and TM genomes, respectively. From diploid TKS to triploid TM, the total number of MADS-box genes did not increase, but expansion occurred in specific subfamilies. Between the two genomes, a total of 11 duplications, which promoted the expansion of MADS-box genes, were identified in the two species. TkMADS and TmMADS were highly conserved, and showed good collinearity. Furthermore, most TkMADS genes exhibiting tissue-specific expression patterns, especially genes associated with the ABCDE model, were preferentially expressed in the flowers, suggesting their conserved and dominant functions in flower development in TKS. Moreover, by comparing the transcriptomes of different TKS lines, we identified 25 TkMADSs related to biomass formation and 4 TkMADSs related to NR content, which represented new targets for improving the NR yield of TKS.

Identification and validation of new MADS-box homologous genes in 3010 rice pan-genome

KEY MESSAGE

Identification and validation of ten new MADS-box homologous genes in 3010 rice pan-genome for rice breeding. The functional genome is significant for rice breeding. MADS-box genes encode transcription factors that are indispensable for rice growth and development. The reported 15,362 novel genes in the rice pan-genome (RPAN) of Asian cultivated rice accessions provided a useful gene reservoir for the identification of more MADS-box candidates to overcome the limitation for the usage of only 75 MADS-box genes identified in Nipponbare for rice breeding. Here, we report the identification and validation of ten MADS-box homologous genes in RPAN. Origin and identity analysis indicated that they are originated from different wild rice accessions and structure of motif analysis revealed high variations in their amino acid sequences. Phylogenetic results with 277 MADS-box genes in 41 species showed that all these ten MADS-box homologous genes belong to type I (SRF-like, M-type). Gene expression analysis confirmed the existence of these ten MADS-box genes in IRIS_313-10,394, all of them were expressed in flower tissues, and six of them were highly expressed during seed development. Altogether, we identified and validated experimentally, for the first time, ten novel MADS-box genes in RPAN, which provides new genetic sources for rice improvement.

Genome-wide analysis of Panax MADS-box genes reveals role of PgMADS41 and PgMADS44 in modulation of root development and ginsenoside synthesis

Panax root is an important material used in food and medicine. Its cultivation and production usually depend on root shape and ginsenoside content. There is limited understanding about the synergistic regulatory mechanisms underlying root development and ginsenoside accumulation in Panax. MADS-box transcription factors possibly play a significant role in regulation of root growth and secondary metabolites. In this study, we identified MADS-box transcription factors of Panax, and found high expression levels of SVP, ANR1 and SOC1-like clade genes in its roots. We confirmed that two SOC1-like genes, PgMADS41 and PgMADS44, bind to expansion gene promoters (PgEXLB5 and PgEXPA13), which contribute to root growth, and to SE-4, CYP716A52v2-4, and β-AS-13 promoters, which participate in ginsenoside Ro biosynthesis. These two genes were found to increase lateral root number and main root length in transgenic Arabidopsis thaliana by improving AtEXLA1, AtEXLA3, AtEXPA5, and AtEXPA6 gene expression. As a non-phytohormone regulatory tool, Ro can stimulate adventitious root growth by influencing their expression and ginsenoside accumulation. Our study provides new insights into the coordinated regulatory function of SOC1-like clade genes in Panax root development and triterpenoid accumulation, paving the way towards understanding root formation and genetic improvement in Panax.

Phenotypic and Genotypic Diversity of Roots Response to Salt in Durum Wheat Seedlings

Soil salinity is a serious threat to food production now and in the near future. In this study, the root system of six durum wheat genotypes, including one highly salt-tolerant (J. Khetifa) used as a check genotype, was evaluated, by a high-throughput phenotyping system, under control and salt conditions at the seedling stage. Genotyping was performed using 11 SSR markers closely linked with genome regions associated with root traits. Based on phenotypic cluster analysis, genotypes were grouped differently under control and salt conditions. Under control conditions, genotypes were clustered mainly due to a root angle, while under salt stress, genotypes were grouped according to their capacity to maintain higher roots length, volume, and surface area, as J. Khetifa, Sebatel, and Azeghar. SSR analysis identified a total of 42 alleles, with an average of about three alleles per marker. Moreover, quite a high number of Private alleles in total, 18 were obtained. The UPGMA phenogram of the Nei (1972) genetic distance clusters for 11 SSR markers and all phenotypic data under control conditions discriminate genotypes almost into the same groups. The study revealed as the combination of high-throughput systems for phenotyping with SSR markers for genotyping it's a useful tool to provide important data for the selection of suitable parental lines for salt-tolerance breeding. Nevertheless, the narrow root angle, which is an important trait in drought tolerance, is not a good indicator of salt tolerance. Instated for salt tolerance is more important the amount of roots.

High Efficiency Regeneration System from Blueberry Leaves and Stems

The main propagation approach is tissue culture in blueberries, and tissue culture is an effective and low-cost method with higher economic efficiency in blueberries. However, there is a lack of stable and efficient production systems of industrialization of tissue culture in blueberries. In this study, the high-efficiency tissue culture and rapid propagation technology system were established based on blueberry leaves and stems. The optimal medium for callus induction was WPM (woody plant medium) containing 2.0 mg/L Forchlorfenuron (CPPU), 0.2 mg/L 2-isopentenyladenine (2-ip) with a 97% callus induction rate and a callus differentiation rate of 71% by using blueberry leaves as explants. The optimal secondary culture of the leaf callus medium was WPM containing 3.0 mg/L CPPU with an increment coefficient of 24%. The optimal bud growth medium was WPM containing 1.0 mg/L CPPU, 0.4 mg/L 2-ip, with which the growth of the bud was better, stronger and faster. The optimal rooting medium was 1/2 Murashige and Skoog (1/2MS) medium containing 2.0 mg/L naphthylacetic acid (NAA), with which the rooting rate was 90% with shorter rooting time and more adventitious root. In addition, we established a regeneration system based on blueberry stems. The optimal preculture medium in blueberry stem explants was MS medium containing 2-(N-morpholino) ethanesulfonic acid (MES) containing 0.2 mg/L indole-3-acetic acid (IAA), 0.1 mg/L CPPU, 100 mg/L NaCl, with which the germination rate of the bud was 93%. The optimal medium for fast plant growth was MS medium containing MES containing 0.4 mg/L zeatin (ZT), 1 mg/L putrescine, 1 mg/L spermidine, 1 mg/L spermidine, which had a good growth state and growth rate. The optimal cultivation for plantlet growth was MS medium containing MES containing 0.5 mg/L isopentene adenine, with which the plantlet was strong. The optimal rooting medium for the stem was 1/2MS medium containing 2.0 mg/L NAA, with which the rooting rate was 93% with a short time and more adventitious root. In conclusion, we found that stem explants had higher regeneration efficiency for a stable and efficient production system of industrialization of tissue culture. This study provides theoretical guidance and technical support in precision breeding and standardization and industrialization in the blueberry industry.

Systematic analysis of MADS-box gene family in the U's triangle species and targeted mutagenesis of BnaAG homologs to explore its role in floral organ identity in Brassica napus

MADS-box transcription factors play an important role in regulating floral organ development and participate in environmental responses. To date, the MADS-box gene family has been widely identified in Brassica rapa (B. rapa), Brassica oleracea (B. oleracea), and Brassica napus (B. napus); however, there are no analogous reports in Brassica nigra (B. nigra), Brassica juncea (B. juncea), and Brassica carinata (B. carinata). In this study, a whole-genome survey of the MADS-box gene family was performed for the first time in the triangle of U species, and a total of 1430 MADS-box genes were identified. Based on the phylogenetic relationship and classification of MADS-box genes in Arabidopsis thaliana (A. thaliana), 1430 MADS-box genes were categorized as M-type subfamily (627 genes), further divided into Mα, Mβ, Mγ, and Mδ subclades, and MIKC-type subfamily (803 genes), further classified into 35 subclades. Gene structure and conserved protein motifs of MIKC-type MADS-box exhibit diversity and specificity among different subclades. Comparative analysis of gene duplication events and syngenic gene pairs among different species indicated that polyploidy is beneficial for MIKC-type gene expansion. Analysis of transcriptome data within diverse tissues and stresses in B. napus showed tissue-specific expression of MIKC-type genes and a broad response to various abiotic stresses, particularly dehydration stress. In addition, four representative floral organ mutants (wtl, feml, aglf-2, and aglf-1) in the T0 generation were generated by editing four AGAMOUS (BnaAG) homoeologs in B. napus that enriched the floral organ variant phenotype. In brief, this study provides useful information for investigating the function of MADS-box genes and contributes to revealing the regulatory mechanisms of floral organ development in the genetic improvement of new varieties.

Genome-Wide Analysis of the Mads-Box Transcription Factor Family in Solanum melongena

The MADS-box transcription factors are known to be involved in several aspects of plant growth and development, especially in floral organ specification. However, little is known in eggplant. Here, 120 eggplant MADS-box genes were identified and categorized into type II (MIKCC and MIKC*) and type I (Mα, Mβ, and Mγ) subfamilies based on phylogenetic relationships. The exon number in type II SmMADS-box genes was greater than that in type I SmMADS-box genes, and the K-box domain was unique to type II MADS-box TFs. Gene duplication analysis revealed that segmental duplications were the sole contributor to the expansion of type II genes. Cis-elements of MYB binding sites related to flavonoid biosynthesis were identified in three SmMADS-box promoters. Flower tissue-specific expression profiles showed that 46, 44, 38, and 40 MADS-box genes were expressed in the stamens, stigmas, petals, and pedicels, respectively. In the flowers of SmMYB113-overexpression transgenic plants, the expression levels of 3 SmMADS-box genes were co-regulated in different tissues with the same pattern. Correlation and protein interaction predictive analysis revealed six SmMADS-box genes that might be involved in the SmMYB113-regulated anthocyanin biosynthesis pathway. This study will aid future studies aimed at functionally characterizing important members of the MADS-box gene family.

Transcriptomics Analysis Reveals a Putative Role for Hormone Signaling and MADS-Box Genes in Mature Chestnut Shoots Rooting Recalcitrance

Maturation imposes several changes in plants, which are particularly drastic in the case of trees. In recalcitrant woody species, such as chestnut (Castanea sativa Mill.), one of the major maturation-related shifts is the loss of the ability to form adventitious roots in response to auxin treatment as the plant ages. To analyze the molecular mechanisms underlying this phenomenon, an in vitro model system of two different lines of microshoots derived from the same field-grown tree was established. While juvenile-like shoots root readily when treated with exogenous auxin, microshoots established from the crown of the tree rarely form roots. In the present study, a transcriptomic analysis was developed to compare the gene expression patterns in both types of shoots 24 h after hormone and wounding treatment, matching the induction phase of the process. Our results support the hypothesis that the inability of adult chestnut tissues to respond to the inductive treatment relies in a deep change of gene expression imposed by maturation that results in a significant transcriptome modification. Differences in phytohormone signaling seem to be the main cause for the recalcitrant behavior of mature shoots, with abscisic acid and ethylene negatively influencing the rooting ability of the chestnut plants. We have identified a set of related MADS-box genes whose expression is modified but not suppressed by the inductive treatment in mature shoots, suggesting a putative link of their activity with the rooting-recalcitrant behavior of this material. Overall, distinct maturation-derived auxin sensibility and homeostasis, and the related modifications in the balance with other phytohormones, seem to govern the outcome of the process in each type of shoots.

SPL12 Regulates AGL6 and AGL21 to Modulate Nodulation and Root Regeneration under Osmotic Stress and Nitrate Sufficiency Conditions in Medicago sativa

The highly conserved plant microRNA, miR156, affects root architecture, nodulation, symbiotic nitrogen fixation, and stress response. In Medicago sativa, transcripts of eleven SQUAMOSA-PROMOTER BINDING PROTEIN-LIKE, SPLs, including SPL12, are targeted for cleavage by miR156. Our previous research revealed the role of SPL12 and its target gene, AGL6, in nodulation in alfalfa. Here, we investigated the involvement of SPL12, AGL6 and AGL21 in nodulation under osmotic stress and different nitrate availability conditions. Characterization of phenotypic and molecular parameters revealed that the SPL12/AGL6 module plays a negative role in maintaining nodulation under osmotic stress. While there was a decrease in the nodule numbers in WT plants under osmotic stress, the SPL12-RNAi and AGL6-RNAi genotypes maintained nodulation under osmotic stress. Moreover, the results showed that SPL12 regulates nodulation under a high concentration of nitrate by silencing AGL21. AGL21 transcript levels were increased under nitrate treatment in WT plants, but SPL12 was not affected throughout the treatment period. Given that AGL21 was significantly upregulated in SPL12-RNAi plants, we conclude that SPL12 may be involved in regulating nitrate inhibition of nodulation in alfalfa by targeting AGL21. Taken together, our results suggest that SPL12, AGL6, and AGL21 form a genetic module that regulates nodulation in alfalfa under osmotic stress and in response to nitrate.

MIKC-type MADS-box transcription factor gene family in peanut: Genome-wide characterization and expression analysis under abiotic stress

Peanut (Arachis hypogaea) is one of the most important economic crops around the world, especially since it provides vegetable oil and high-quality protein for humans. Proteins encoded by MADS-box transcription factors are widely involved in regulating plant growth and development as well as responses to abiotic stresses. However, the MIKC-type MADS-box TFs in peanut remains currently unclear. Hence, in this study, 166 MIKC-type MADS-box genes were identified in both cultivated and wild-type peanut genomes, which were divided into 12 subfamilies. We found a variety of development-, hormone-, and stress-related cis-acting elements in the promoter region of peanut MIKC-type MADS-box genes. The chromosomal distribution of peanut MADS-box genes was not random, and gene duplication contributed to the expansion of the MADS-box gene family. The interaction network of the peanut AhMADS proteins was established. Expression pattern analysis showed that AhMADS genes were specifically expressed in tissues and under abiotic stresses. It was further confirmed via the qRT-PCR technique that five selected AhMADS genes could be induced by abiotic and hormone treatments and presented different expressive profiles under various stresses. Taken together, these findings provide valuable information for the exploration of candidate genes in molecular breeding and further study of AhMADS gene functions.

Comparative Transcriptome Profiling Reveals Potential Candidate Genes, Transcription Factors, and Biosynthetic Pathways for Phosphite Response in Potato (Solanum tuberosum L.)

The study was conducted with C31 and C80 genotypes of the potato (Solanum tuberosum L.), which are tolerant and susceptible to phosphite (Phi, H₂PO₃), respectively. To decipher the molecular mechanisms underlying tolerance and susceptibility to Phi in the potato, RNA sequencing was used to study the global transcriptional patterns of the two genotypes. Media were prepared with 0.25 and 0.50 mM Phi, No-phosphorus (P), and 1.25 mM (phosphate, Pi as control). The values of fragments per kilobase of exon per million mapped fragments of the samples were also subjected to a principal component analysis, grouping the biological replicates of each sample. Using stringent criteria, a minimum of 819 differential (DEGs) were detected in both C80-Phi-0.25_vs_C80-Phi-0.50 (comprising 517 upregulated and 302 downregulated) and C80-Phi-0.50_vs_C80-Phi-0.25 (comprising 302 upregulated and 517 downregulated) and a maximum of 5214 DEGs in both C31-Con_vs_C31-Phi-0.25 (comprising 1947 upregulated and 3267 downregulated) and C31-Phi-0.25_vs_C31-Con (comprising 3267 upregulated and 1947 downregulated). DEGs related to the ribosome, plant hormone signal transduction, photosynthesis, and plant–pathogen interaction performed important functions under Phi stress, as shown by the Kyoto Encyclopedia of Genes and Genomes annotation. The expressions of transcription factors increased significantly in C31 compared with C80. For example, the expressions of Soltu.DM.01G047240, Soltu.DM.08G015900, Soltu.DM.06G012130, and Soltu.DM.08G012710 increased under P deficiency conditions (Phi-0.25, Phi-0.50, and No-P) relative to the control (P sufficiency) in C31. This study adds to the growing body of transcriptome data on Phi stress and provides important clues to the Phi tolerance response of the C31 genotype.

Regulatory network for FOREVER YOUNG FLOWER-like genes in regulating Arabidopsis flower senescence and abscission

FOREVER YOUNG FLOWER (FYF) has been reported to play an important role in regulating flower senescence/abscission. Here, we functionally analyzed five Arabidopsis FYF-like genes, two in the FYF subgroup (FYL1/AGL71 and FYL2/AGL72) and three in the SOC1 subgroup (SOC1/AGL20, AGL19, and AGL14/XAL2), and showed their involvement in the regulation of flower senescence and/or abscission. We demonstrated that in FYF subgroup, FYF has both functions in suppressing flower senescence and abscission, FYL1 only suppresses flower abscission and FYL2 has been converted as an activator to promote flower senescence. In SOC1 subgroup, AGL19/AGL14/SOC1 have only one function in suppressing flower senescence. We also found that FYF-like proteins can form heterotetrameric complexes with different combinations of A/E functional proteins (such as AGL6 and SEP1) and AGL15/18-like proteins to perform their functions. These findings greatly expand the current knowledge behind the multifunctional evolution of FYF-like genes and uncover their regulatory network in plants.

Nitrate-dependent regulation of miR444-OsMADS27 signalling cascade controls root development in rice

Nitrate is an important nutrient and a key signalling molecule for plant development. A number of transcription factors involved in the response to nitrate and their regulatory mechanisms have been identified. However, little is known about the transcription factors involved in nitrate sensing and their regulatory mechanisms among crop plants. In this study, we identified functions of a nitrate-responsive miR444:MADS-box transcription factor OsMADS27 module and its downstream targets mediating rice root growth and stress responses. Transgenic rice plants expressing miR444 target mimic improved rice root growth. Although miR444 has the potential to target multiple genes, we identified OsMADS27 as the major miR444 target that regulates the expression of nitrate transporters, as well as several key genes including expansins, and those associated with auxin signalling, to promote root growth. In agreement with this, overexpression of miRNA-resistant OsMADS27 improved root development and tolerance to abiotic stresses, while its silencing suppressed root growth. OsMADS27 mediated robust stress tolerance in plants through its ability to bind to the promoters of specific stress regulators, as observed in ChIP-seq analysis. Our results provide evidence of a nitrate-dependent miR444-OsMADS27 signalling cascade involved in the regulation of rice root growth, as well as its surprising role in stress responses.

The rolB-transgenic Nicotiana tabacum plants exhibit upregulated ARF7 and ARF19 gene expression

Agrobacterium rhizogenes root oncogenic locus B (rolB) is known to induce hairy roots along with triggering several physiological and morphological changes when present as a transgene. However, it is still unknown how this gene triggers these changes within the plant system. In this study, the effect of rolB in-planta, when present as a transgene, was assessed on the gene expression levels of auxin response factors (ARFs)-transcription factors which are key players in auxin-mediated responses. The goal was to uncover Auxin/ARF-driven transcriptional networks potentially active and working selectively, if any, in rolB transgenic background, which might potentially be associated with hairy root development. Hence, the approach involved establishing rolB-transgenic Nicotiana tabacum plants, selecting ARFs (NtARFs) for context-relevance using bioinformatics followed by gene expression profiling. It was observed that out of the chosen NtARFs, NtARF7 and NtARF19 exhibited a consistent pattern of gene upregulation across organ types. In order to understand the significance of these selective gene upregulation, ontology-based transcriptional network maps of the differentially and nondifferentially expressed ARFs were constructed, guided by co-expression databases. The network maps suggested that NtARF7-NtARF19 might have major deterministic, underappreciated roles to play in root development in a rolB-transgenic background-as observed by higher number of "root-related" biological processes present as nodes compared to network maps for similarly constructed other non-differentially expressed ARFs. Based on the inferences drawn, it is hypothesized that rolB, when present as a transgene, might drive hairy root development by selective induction of NtARF7 and NtARF19, suggesting a functional link between the two, leading to the specialized and characteristic rolB-associated traits.

Regulation of the Later Stages of Nodulation Stimulated by IPD3/CYCLOPS Transcription Factor and Cytokinin in Pea Pisum sativum L

The IPD3/CYCLOPS transcription factor was shown to be involved in the regulation of nodule primordia development and subsequent stages of nodule differentiation. In contrast to early stages, the stages related to nodule differentiation remain less studied. Recently, we have shown that the accumulation of cytokinin at later stages may significantly impact nodule development. This conclusion was based on a comparative analysis of cytokinin localization between pea wild type and ipd3/cyclops mutants. However, the role of cytokinin at these later stages of nodulation is still far from understood. To determine a set of genes involved in the regulation of later stages of nodule development connected with infection progress, intracellular accommodation, as well as plant tissue and bacteroid differentiation, the RNA-seq analysis of pea mutant SGEFix--2 (sym33) nodules impaired in these processes compared to wild type SGE nodules was performed. To verify cytokinin's influence on late nodule development stages, the comparative RNA-seq analysis of SGEFix--2 (sym33) mutant plants treated with cytokinin was also conducted. Findings suggest a significant role of cytokinin in the regulation of later stages of nodule development.

Arabidopsis MADS-box factor AGL16 is a negative regulator of plant response to salt stress by downregulating salt-responsive genes

Sessile plants constantly experience environmental stresses in nature. They must have evolved effective mechanisms to balance growth with stress response. Here we report the MADS-box transcription factor AGL16 acting as a negative regulator in stress response in Arabidopsis. Loss-of-AGL16 confers resistance to salt stress in seed germination, root elongation and soil-grown plants, while elevated AGL16 expression confers the opposite phenotypes compared with wild-type. However, the sensitivity to abscisic acid (ABA) in seed germination is inversely correlated with AGL16 expression levels. Transcriptomic comparison revealed that the improved salt resistance of agl16 mutants was largely attributed to enhanced expression of stress-responsive transcriptional factors and the genes involved in ABA signalling and ion homeostasis. We further demonstrated that AGL16 directly binds to the CArG motifs in the promoter of HKT1;1, HsfA6a and MYB102 and represses their expression. Genetic analyses with double mutants also support that HsfA6a and MYB102 are target genes of AGL16. Taken together, our results show that AGL16 acts as a negative regulator transcriptionally suppressing key components in the stress response and may play a role in balancing stress response with growth.

Differential expression pattern of novel MADS-box genes in early root formation and differentiation of sweet potato

MADS-box genes are important transcription factors affecting overall development, but their role in sweet potato [Ipomoea batatas (L.) Lam.] has not been fully studied. This study isolated six novel MADS-box genes (IbSOC1, IbFUL1, IbAGL6, IbSVP1, IbSVP2, and IbSVP3) from sweet potato [Ipomoea batatas (L.) Lam. cv. Annouimo] during the early root differentiation stage using the de novo transcriptome assembly sequencing method. At the early root differentiation (between 0 and 3 days after transplanting), the IbSOC1, IbFUL1, and IbSVP2 genes decreased rapidly, whereas the IbSVP3 gene decreased gradually. In the early stages of root formation (0-30 days), the levels of IbSVP1 and IbSVP3 expression were steady, but the levels of IbSOC1 expression decreased gradually. The expression of six novel genes was also conducted in the tuberous root formation stage (30-90 days), and the IbSVP3 gene increased significantly according to the formation of the tuberous root. Six novel MADS-box genes that were believed to influence the entire root formation of sweet potato were isolated from the sweet potato. This study provides a genetic basis for further research on sweet potato root formation and development.

The Gillenia trifoliata genome reveals dynamics correlated with growth and reproduction in Rosaceae

The Rosaceae family has striking phenotypic diversity and high syntenic conservation. Gillenia trifoliata is sister species to the Maleae tribe of apple and ~1000 other species. Gillenia has many putative ancestral features, such as herb/sub-shrub habit, dry fruit-bearing and nine base chromosomes. This coalescence of ancestral characters in a phylogenetically important species, positions Gillenia as a 'rosetta stone' for translational science within Rosaceae. We present genomic and phenological resources to facilitate the use of Gillenia for this purpose. The Gillenia genome is the first fully annotated chromosome-level assembly with an ancestral genome complement (x = 9), and with it we developed an improved model of the Rosaceae ancestral genome. MADS and NAC gene family analyses revealed genome dynamics correlated with growth and reproduction and we demonstrate how Gillenia can be a negative control for studying fleshy fruit development in Rosaceae.

A rice transcription factor, OsMADS57, positively regulates high salinity tolerance in transgenic Arabidopsis thaliana and Oryza sativa plants

MADS-box transcription factors (TFs) play indispensable roles in various aspects of plant growth, development as well as in response to environmental stresses. Several MADS-box genes have been reported to be involved in the salt tolerance in different plant species. However, the role of the transcription factor OsMADS57 under salinity stress is still unknown. Here, the results of this study showed that OsMADS57 was mainly expressed in roots and leaves of rice plants (Oryza sativa). Gene expression pattern analysis revealed that OsMADS57 was induced by NaCl. Overexpression of OsMADS57 in both Arabidopsis thaliana (A. thaliana) and rice could improve their salt tolerance, which was demonstrated by higher germination rates, longer root length and better growth status of overexpression plants than wild type (WT) under salinity conditions. In contrast, RNA interference (RNAi) lines of rice showed more sensitivity towards salinity. Moreover, less reactive oxygen species (ROS) accumulated in OsMADS57 overexpressing lines when exposed to salt stress, as measured by 3, 3'-diaminobenzidine (DAB) or nitroblue tetrazolium (NBT) staining. Further experiments exhibited that overexpression of OsMADS57 in rice significantly increased the tolerance ability of plants to oxidative damage under salt stress, mainly by increasing the activities of antioxidative enzymes such as superoxide dismutase (SOD) and peroxidase (POD), reducing malonaldehyde (MDA) content and improving the expression of stress-related genes. Taken together, these results demonstrated that OsMADS57 plays a positive role in enhancing salt tolerance by activating the antioxidant system.

GmFULa improves soybean yield by enhancing carbon assimilation without altering flowering time or maturity

KEY MESSAGE

GmFULa improved soybean yield by enhancing carbon assimilation. Meanwhile, different from known yield-related genes, it did not alter flowering time or maturity. Soybean (Glycine max (L.) Merr.) is highly demanded by a continuously growing human population. However, increasing soybean yield is a major challenge. FRUITFULL (FUL), a MADS-box transcription factor, plays important roles in multiple developmental processes, especially fruit and pod development, which are crucial for soybean yield formation. However, the functions of its homologs in soybean are not clear. Here, through haplotype analysis, we found that one haplotype of the soybean homolog GmFULa (GmFULa-H02) is dominant in cultivated soybeans, suggesting that GmFULa-H02 was highly selected during domestication and varietal improvement of soybean. Interestingly, transgenic overexpression of GmFULa enhanced vegetative growth with more biomass accumulated and ultimately increased the yield but without affecting the plant height or changing the flowering time and maturity, indicating that it enhances the efficiency of dry matter accumulation. It also promoted the yield factors like branch number, pod number and 100-seed weight, which ultimately increased the yield. It increased the palisade tissue cell number and the chlorophyll content to promote photosynthesis and increase the soluble sugar content in leaves and fresh seeds. Furthermore, GmFULa were found to be sublocalized in the nucleus and positively regulate sucrose synthases (SUSs) and sucrose transporters (SUTs) by binding with the conserved CArG boxes in their promoters. Overall, these results showed GmFULa promotes the capacity of assimilation and the transport of the resultant assimilates to increase yield, and provided insights into the link between GmFULa and sucrose synthesis with transport-related molecular pathways that control seed yield.

Control of the Rhizobia Nitrogen-Fixing Symbiosis by Common Bean MADS-Domain/AGL Transcription Factors

Plants MADS-domain/AGL proteins constitute a large transcription factor (TF) family that controls the development of almost every plant organ. We performed a phylogeny of (ca. 500) MADS-domain proteins from Arabidopsis and four legume species. We identified clades with Arabidopsis MADS-domain proteins known to participate in root development that grouped legume MADS-proteins with similar high expression in roots and nodules. In this work, we analyzed the role of AGL transcription factors in the common bean (Phaseolus vulgaris) - Rhizobium etli N-fixing symbiosis. Sixteen P. vulgaris AGL genes (PvAGL), out of 93 family members, are expressed - at different levels - in roots and nodules. From there, we selected the PvAGL gene denominated PvFUL-like for overexpression or silencing in composite plants, with transgenic roots and nodules, that were used for phenotypic analysis upon inoculation with Rhizobium etli. Because of sequence identity in the DNA sequence used for RNAi-FUL-like construct, roots, and nodules expressing this construct -referred to as RNAi_AGL- showed lower expression of other five PvAGL genes highly expressed in roots/nodules. Contrasting with PvFUL-like overexpressing plants, rhizobia-inoculated plants expressing the RNAi_AGL silencing construct presented affection in the generation and growth of transgenic roots from composite plants, both under non-inoculated or rhizobia-inoculated condition. Furthermore, the rhizobia-inoculated plants showed decreased rhizobial infection concomitant with the lower expression level of early symbiotic genes and increased number of small, ineffective nodules that indicate an alteration in the autoregulation of the nodulation symbiotic process. We propose that the positive effects of PvAGL TF in the rhizobia symbiotic processes result from its potential interplay with NIN, the master symbiotic TF regulator, that showed a CArG-box consensus DNA sequence recognized for DNA binding of AGL TF and presented an increased or decreased expression level in roots from non-inoculated plants transformed with OE_FUL or RNAi_AGL construct, respectively. Our work contributes to defining novel transcriptional regulators for the common bean - rhizobia N-fixing symbiosis, a relevant process for sustainable agriculture.

Nepenthes × ventrata Transcriptome Profiling Reveals a Similarity Between the Evolutionary Origins of Carnivorous Traps and Floral Organs

The emergence of the carnivory syndrome and traps in plants is one of the most intriguing questions in evolutionary biology. In the present study, we addressed it by comparative transcriptomics analysis of leaves and leaf-derived pitcher traps from a predatory plant Nepenthes ventricosa × Nepenthes alata. Pitchers were collected at three stages of development and a total of 12 transcriptomes were sequenced and assembled de novo. In comparison with leaves, pitchers at all developmental stages were found to be highly enriched with upregulated genes involved in stress response, specification of shoot apical meristem, biosynthesis of sucrose, wax/cutin, anthocyanins, and alkaloids, genes encoding digestive enzymes (proteases and oligosaccharide hydrolases), and flowering-related MADS-box genes. At the same time, photosynthesis-related genes in pitchers were transcriptionally downregulated. As the MADS-box genes are thought to be associated with the origin of flower organs from leaves, we suggest that Nepenthes species could have employed a similar pathway involving highly conserved MADS-domain transcription factors to develop a novel structure, pitcher-like trap, for capture and digestion of animal prey during the evolutionary transition to carnivory. The data obtained should clarify the molecular mechanisms of trap initiation and development and may contribute to solving the problem of its emergence in plants.

Genetic control of root plasticity in response to salt stress in maize

GWAS identified 559 significant SNPs associated with the remodelling of the root architecture in response to salt, and 168 candidate genes were prioritized by integrating RNA-seq, DEG and WGCNA data. Salinity is a major environmental factor limiting crop growth and productivity. The root is the first plant organ to encounter salt stress, yet the effects of salinity on maize root development remain unclear. In this study, the natural variations in 14 root and 4 shoot traits were evaluated in 319 maize inbred lines under control and saline conditions. Considerable phenotypic variations were observed for all traits, with high salt concentrations decreasing the root length, but increasing the root diameter. A genome-wide association study was conducted to analyse these traits and their plasticity (relative variation). We detected 559 significant single nucleotide polymorphisms, of which 125, 181 and 253 were associated with the control condition, stress condition and trait plasticity, respectively. A total of 168 of 587 candidate genes identified by genome-wide association study were supported by the differentially expressed genes or co-expression networks. Two candidate genes ZmIAA1 and ZmGRAS43 were validated by resequencing. Among these genes, 130 were detected under stress condition or trait plasticity that involved in diverse biological processes including plant hormone signal transduction, phenylpropanoid biosynthesis and fatty acid biosynthesis. Our findings clarify the root remodelling to salinity, and the identified loci and candidate genes may be important for the genetic improvement of root traits and salt tolerance in maize.

Genetic regulation of the traits contributing to wheat nitrogen use efficiency

High nitrogen application aimed at increasing crop yield is offset by higher production costs and negative environmental consequences. For wheat, only one third of the applied nitrogen is utilized, which indicates there is scope for increasing Nitrogen Use Efficiency (NUE). However, achieving greater NUE is challenged by the complexity of the trait, which comprises processes associated with nitrogen uptake, transport, reduction, assimilation, translocation and remobilization. Thus, knowledge of the genetic regulation of these processes is critical in increasing NUE. Although primary nitrogen uptake and metabolism-related genes have been well studied, the relative influence of each towards NUE is not fully understood. Recent attention has focused on engineering transcription factors and identification of miRNAs acting on expression of specific genes related to NUE. Knowledge obtained from model species needs to be translated into wheat using recently-released whole genome sequences, and by exploring genetic variations of NUE-related traits in wild relatives and ancient germplasm. Recent findings indicate the genetic basis of NUE is complex. Pyramiding various genes will be the most effective approach to achieve a satisfactory level of NUE in the field.

Regulator Network Analysis of Rice and Maize Yield-Related Genes

Rice and maize are the principal food crop species worldwide. The mechanism of gene regulation for the yield of rice and maize is still the research focus at present. Seed size, weight and shape are important traits of crop yield in rice and maize. Most members of three gene families, APETALA2/ethylene response factor, auxin response factors and MADS, were identified to be involved in yield traits in rice and maize. Analysis of molecular regulation mechanisms related to yield traits provides theoretical support for the improvement of crop yield. Genetic regulatory network analysis can provide new insights into gene families with the improvement of sequencing technology. Here, we analyzed the evolutionary relationships and the genetic regulatory network for the gene family members to predicted genes that may be involved in yield-related traits in rice and maize. The results may provide some theoretical and application guidelines for future investigations of molecular biology, which may be helpful for developing new rice and maize varieties with high yield traits.

Characteristics of banana B genome MADS-box family demonstrate their roles in fruit development, ripening, and stress

MADS-box genes are critical regulators of growth and development in flowering plants. Sequencing of the Musa balbisiana (B) genome has provided a platform for the systematic analysis of the MADS-box gene family in the important banana ancestor Musa balbisiana. Seventy-seven MADS-box genes, including 18 type I and 59 type II, were strictly identified from the banana (Pisang Klutuk Wulung, PKW, 2n = 2x = 22) B genome. These genes have been preferentially placed on the banana B genome. Evolutionary analysis suggested that M. balbisiana MCM1-AGAMOUS-DEFICIENS-SRF (MbMADS) might be organized into the MIKC^c, MIKC*, Mα, Mβ, and Mγ groups according to the phylogeny. MIKC^c was then further categorized into 10 subfamilies according to conserved motif and gene structure analyses. The well-defined MADS-box genes highlight gene birth and death in banana. MbMADSes originated from the same ancestor as MaMADSes. Transcriptome analysis in cultivated banana (ABB) revealed that MbMADSes were conserved and differentially expressed in several organs, in various fruit developing and ripening stages, and in stress treatments, indicating the participation of these genes in fruit development, ripening, and stress responses. Of note, SEP/AGL2 and AG, as well as other several type II MADS-box genes, including the STMADS11 and TM3/SOC1 subfamilies, indicated elevated expression throughout banana fruit development, ripening, and stress treatments, indicating their new parts in controlling fruit development and ripening. According to the co-expression network analysis, MbMADS75 interacted with bZIP and seven other transcription factors to perform its function. This systematic analysis reveals fruit development, ripening, and stress candidate MbMADSes genes for additional functional studies in plants, improving our understanding of the transcriptional regulation of MbMADSes genes and providing a base for genetic modification of MADS-mediated fruit development, ripening, and stress.

Molecular basis for neofunctionalization of duplicated E3 ubiquitin ligases underlying adaptation to drought tolerance in Arabidopsis thaliana

Multigene families in plants expanded from ancestral genes via gene duplication mechanisms constitute a significant fraction of the coding genome. Although most duplicated genes are lost over time, many are retained in the genome. Clusters of tandemly arrayed genes are commonly found in the plant genome where they can promote expansion of gene families. In the present study, promoter fusion to the GUS reporter gene was used to examine the promoter architecture of duplicated E3 ligase genes that are part of group C in the Arabidopsis thaliana ATL family. Acquisition of gene expression by AtATL78, possibly generated from defective AtATL81 expression, is described. AtATL78 expression was purportedly enhanced by insertion of a TATA box within the core promoter region after a short tandem duplication that occurred during evolution of Brassicaceae lineages. This gene is associated with an adaptation to drought tolerance of A. thaliana. These findings also suggest duplicated genes could serve as a reservoir of tacit genetic information, and expression of these duplicated genes is activated upon acquisition of core promoter sequences. Remarkably, drought transcriptome profiling in response to rehydration suggests that ATL78-dependent gene expression predominantly affects genes with root-specific activities.

Identification, characterization and functional analysis of AGAMOUS subfamily genes associated with floral organs and seed development in Marigold (Tagetes erecta)

BACKGROUND

AGAMOUS (AG) subfamily genes regulate the floral organs initiation and development, fruit and seed development. At present, there has been insufficient study of the function of AG subfamily genes in Asteraceae. Marigold (Tagetes erecta) belongs to Asteraceae family whose unique inflorescence structure makes it an important research target for understanding floral organ development in plants.

RESULTS

Four AG subfamily genes of marigold were isolated and phylogenetically grouped into class C (TeAG1 and TeAG2) and class D (TeAGL11-1 and TeAGL11-2) genes. Expression profile analysis demonstrated that these four genes were highly expressed in reproductive organs of marigold. Subcellular localization analysis suggested that all these four proteins were located in the nucleus. Protein-protein interactions analysis indicated that class C proteins had a wider interaction manner than class D proteins. Function analysis of ectopic expression in Arabidopsis thaliana revealed that TeAG1 displayed a C function specifying the stamen identity and carpel identity, and that TeAGL11-1 exhibited a D function regulating seed development and petal development. In addition, overexpression of both TeAG1 and TeAGL11-1 leaded to curling rosette leaf and early flowering in Arabidopsis thaliana.

CONCLUSIONS

This study provides an insight into molecular mechanism of AG subfamily genes in Asteraceae species and technical support for improvement of several floral traits.

Involvement of a truncated MADS-box transcription factor ZmTMM1 in root nitrate foraging

Plants can develop root systems with distinct anatomical features and morphological plasticity to forage nutrients distributed heterogeneously in soils. Lateral root proliferation is a typical nutrient-foraging response to a local supply of nitrate, which has been investigated across many plant species. However, the underlying mechanism in maize roots remains largely unknown. Here, we report on identification of a maize truncated MIKC-type MADS-box transcription factor (ZmTMM1) lacking K- and C-domains, expressed preferentially in the lateral root branching zone and induced by the localized supply of nitrate. ZmTMM1 belongs to the AGL17-like MADS-box transcription factor family that contains orthologs of ANR1, a key regulator for root nitrate foraging in Arabidopsis. Ectopic overexpression of ZmTMM1 recovers the defective growth of lateral roots in the Arabidopsis anr1 agl21 double mutant. The local activation of glucocorticoid receptor fusion proteins for ZmTMM1 and an artificially truncated form of AtANR1 without the K- and C-domains stimulates the lateral root growth of the Arabidopsis anr1 agl21 mutant, providing evidence that ZmTMM1 encodes a functional MADS-box that modulates lateral root development. However, no phenotype was observed in ZmTMM1-RNAi transgenic maize lines, suggesting a possible genetic redundancy of ZmTMM1 with other AGL17-like genes in maize. A comparative genome analysis further suggests that a nitrate-inducible transcriptional regulation is probably conserved in both truncated and non-truncated forms of ZmTMM1-like MADS-box transcription factors found in grass species.

Overexpression of MADS-box Gene AGAMOUS-LIKE 12 Activates Root Development in Juglans sp. and Arabidopsis thaliana

Until recently, the roles of plant MADS-box genes have mainly been characterized during inflorescence and flower differentiation. In order to precise the roles of AGAMOUS-LIKE 12, one of the few MADS-box genes preferentially expressed in roots, we placed its cDNA under the control of the double 35S CaMV promoter to produce transgenic walnut tree and Arabidopsis plants. In Juglans sp., transgenic somatic embryos showed significantly higher germination rates but abnormal development of their shoot apex prevented their conversion into plants. In addition, a wide range of developmental abnormalities corresponding to ectopic root-like structures affected the transgenic lines suggesting partial reorientations of the embryonic program toward root differentiation. In Arabidopsis, AtAGL12 overexpression lead to the production of faster growing plants presenting dramatically wider and shorter root phenotypes linked to increased meristematic cell numbers within the root apex. In the upper part of the roots, abnormal cell divisions patterns within the pericycle layer generated large ectopic cell masses that did not prevent plants to grow. Taken together, our results confirm in both species that AGL12 positively regulates root meristem cell division and promotes overall root vascular tissue formation. Genetic engineering of AGL12 expression levels could be useful to modulate root architecture and development.

Effect of wet storage conditions on potato tuber transcriptome, phytohormones and growth

BACKGROUND

Stored potato (Solanum tuberosum L.) tubers are sensitive to wet conditions that can cause rotting in long-term storage. To study the effect of water on the tuber surface during storage, microarray analysis, RNA-Seq profiling, qRT-PCR and phytohormone measurements were performed to study gene expression and hormone content in wet tubers incubated at two temperatures: 4 °C and 15 °C. The growth of the plants was also observed in a greenhouse after the incubation of tubers in wet conditions.

RESULTS

Wet conditions induced a low-oxygen response, suggesting reduced oxygen availability in wet tubers at both temperatures when compared to that in the corresponding dry samples. Wet conditions induced genes coding for heat shock proteins, as well as proteins involved in fermentative energy production and defense against reactive oxygen species (ROS), which are transcripts that have been previously associated with low-oxygen stress in hypoxic or anoxic conditions. Wet treatment also induced senescence-related gene expression and genes involved in cell wall loosening, but downregulated genes encoding protease inhibitors and proteins involved in chloroplast functions and in the biosynthesis of secondary metabolites. Many genes involved in the production of phytohormones and signaling were also affected by wet conditions, suggesting altered regulation of growth by wet conditions. Hormone measurements after incubation showed increased salicylic acid (SA), abscisic acid (ABA) and auxin (IAA) concentrations as well as reduced production of jasmonate 12-oxo-phytodienoic acid (OPDA) in wet tubers. After incubation in wet conditions, the tubers produced fewer stems and more roots compared to controls incubated in dry conditions.

CONCLUSIONS

In wet conditions, tubers invest in ROS protection and defense against the abiotic stress caused by reduced oxygen due to excessive water. Changes in ABA, SA and IAA that are antagonistic to jasmonates affect growth and defenses, causing induction of root growth and rendering tubers susceptible to necrotrophic pathogens. Water on the tuber surface may function as a signal for growth, similar to germination of seeds.