Small Auxin Up RNA (SAUR) gene family identification and functional genes exploration during the floral organ and fruit developmental stages in pineapple (Ananas comosus L.) and its response to salinity and drought stresses.

In plants, sexual reproduction relies on the proper development of floral organs that facilitate the successful development of fruits and seeds. Auxin responsive small auxin-up RNA (SAUR) genes play essential roles in floral organ formation and fruit development. However, little is known about the role of SAUR genes in pineapple floral organ formation and fruit development as well as stress responses. In this study, based on genome information and transcriptome datasets, 52 AcoSAUR genes were identified and grouped into 12 groups. The gene structure analysis revealed that most AcoSAUR genes did not have introns, although auxin-acting elements were abundant in the promoter region of AcoSAUR members. The expression analysis across the multiple flower and fruit development stages revealed differential expression of AcoSAUR genes, indicating a tissue and stage-specific function of AcoSAURs. Correlation analysis and pairwise comparisons between gene expression and tissue specificity identified stamen-, petal-, ovule-, and fruit-specific AcoSAURs involved in pineapple floral organs (AcoSAUR4/5/15/17/19) and fruit development (AcoSAUR6/11/36/50). RT-qPCR analysis revealed that AcoSAUR12/24/50 played positive roles in response to the salinity and drought treatment. This work provides an abundant genomic resource for functional analysis of AcoSAUR genes during the pineapple floral organs and fruit development stages. It also highlights the role of auxin signaling involved in pineapple reproductive organ growth.

Genomic insights of the WRKY genes in kenaf (Hibiscus cannabinus L.) reveal that HcWRKY44 improves the plant's tolerance to the salinity stress.

The WRKY transcription factors (TFs) are among the most diverse TF families of plants. They are implicated in various processes related to plant growth and stress response. Kenaf (Hibiscus cannabinus L.), an important fiber crop, has many applications, including the phytoremediation of saline-alkaline soil. However, the roles of WRKY TFs in kenaf are rarely studied. In the present study, 46 kenaf WRKY genes were genome-widely identified and characterized by gene structure, phylogeny and expression pattern analysis. Furthermore, the HcWRKY44 gene was functionally characterized in Arabidopsis under salinity and drought stresses. HcWRKY44 is a nuclear-localized protein that is positively induced by salinity and drought, with roots showing maximum accumulation of its transcripts. Under NaCl and abscisic acid (ABA) stress conditions, plants overexpressing HcWRKY44 had higher germination rates, better root growth and increased survival than control plants; however, it did not improve the ability to withstand drought stress. Moreover, ABA signaling genes (ABI1, ABI2, and ABI5), ABA-responsive genes (ABF4, RD29B, COR15A, COR47, and RD22), stress-related genes (STZ, P5CS, and KIN1), and ionic homeostasis-related genes (SOS1, AHA1, AHA2, and HKT1) were positively induced in HcWRKY44 transgenic plants under NaCl treatment. These results suggest that HcWRKY44 improved plant's tolerance to salt stress but not osmotic stress through an ABA-mediated pathway. In summary, this study provides provided comprehensive information about HcWRKY genes and revealed that HcWRKY44 is involved in salinity tolerance and ABA signaling.

Comparative Expression Profiling of Snf2 Family Genes During Reproductive Development and Stress Responses in Rice.

Sucrose non-fermenting 2 (Snf2) protein family, as chromatin remodeling factors, is an enormous and the most diverse protein family, which contributes to biological processes of replication, transcription, and DNA repair using the energy of adenosine triphosphate (ATP) hydrolysis. The members of Snf2 family proteins have been well characterized in Arabidopsis, rice, and tomato. Although this family received significant attention, few genes were identified uniquely for their roles in mediating reproductive development and stress tolerance in rice. In the present study, we comprehensively analyzed the expression profiling of Snf2 genes during reproductive development and biotic/abiotic stresses. Our results showed that five proteins (OsCHR712/715/720/726/739) were mainly localized in the nucleus, while OsCHR715/739 were also slightly expressed in the cell membrane. There were abundant cis-acting elements in the putative promoter of Snf2 genes, including dehydration, MeJA, MYB binding site for drought, ABA-responsive, and stress-responsive element. Most of the genes were induced immediately after Magnaporthe oryzae infection at 12 h post-infection (hpi). About 55% of the total genes were upregulated under salt and drought stresses during the entire time, and 22-35% of the total genes were upregulated at 3 h. It was noteworthy that the seven genes (OsCHR705, OsCHR706, OsCHR710, OsCHR714, OsCHR721, OsCHR726, and OsCHR737) were upregulated, and one gene (OsCHR712) was downregulated under salt and drought stresses, respectively. The deficiency of OsCHR726 mutations displayed a hypersensitive phenotype under salt stress. These results will be significantly useful features for the validation of the rice Snf2 genes and facilitate understanding of the genetic engineering of crops with improved biotic and abiotic stresses.

OsDDM1b Controls Grain Size by Influencing Cell Cycling and Regulating Homeostasis and Signaling of Brassinosteroid in Rice.

Snf2 family proteins are the crucial subunits of chromatin-remodeling complexes (CRCs), which contributes to the biological processes of transcription, replication, and DNA repair using ATP as energy. Some CRC subunits have been confirmed to be the critical regulators in various aspects of plant growth and development and in epigenetic mechanisms such as histone modification, DNA methylation, and histone variants. However, the functions of Snf2 family genes in rice were poorly investigated. In this study, the relative expression profile of 40 members of Snf2 family in rice was studied at certain developmental stages of seed. Our results revealed that OsCHR741/OsDDM1b (Decrease in DNA methylation 1) was accumulated highly in the early developmental stage of seeds. We further analyzed the OsDDM1b T-DNA insertion loss-of-function of mutant, which exhibited dwarfism, smaller organ size, and shorter and wider grain size than the wild type (Hwayoung, HY), yet no difference in 1,000-grain weight. Consistent with the grain size, the outer parenchyma cell layers of lemma in osddm1b developed more cells with decreased size. OsDDM1b encoded a nucleus, membrane-localized protein and was distributed predominately in young spikelets and seeds, asserting its role in grain size. Meanwhile, the osddm1b was less sensitive to brassinosteroids (BRs) while the endogenous BR levels increased. We detected changes in the expression levels of the BR signaling pathway and feedback-inhibited genes with and without exogenous BR application, and the alterations of expression were also observed in grain size-related genes in the osddm1b. Altogether, our results suggest that OsDDM1b plays a crucial role in grain size via influencing cell proliferation and regulating BR signaling and homeostasis.

Expression characterization and cross-species complementation uncover the functional conservation of YABBY genes for leaf abaxial polarity and carpel polarity establishment in Saccharum spontaneum.

BACKGROUND: Cell polarity establishment and maintenance is indispensable for plant growth and development. In plants, the YABBY transcription factor family has a distinct role in leaf asymmetric polarity establishment and lateral organ initiation. However, for the important sugar crop Saccharum, little information on YABBY genes is available. RESULTS: In this study, a total of 20 sequences for 7 SsYABBY genes were identified in the sugarcane genome, designated as SsYABBY1-7 based on their chromosome locations, and characterized by phylogenetic analysis. We provided a high-resolution map of SsYABBYs' global expression dynamics during vegetative and reproductive organ morphogenesis and revealed that SsYABBY3/4/5 are predominately expressed at the seedling stage of stem and leaf basal zone; SsYABBY2/5/7 are highly expressed in ovules. Besides, cross-species overexpression and/or complementation verified the conserved function of SsYABBY2 in establishing leaf adaxial-abaxial polarity and ovules development. We found that the SsYABBY2 could successfully rescue the leaves curling, carpel dehiscence, and ovule abortion defects in Arabidopsis crc mutant. CONCLUSIONS: Collectively, our study demonstrates that SsYABBY genes retained a conserved function in establishing and preserving leaf adaxial-abaxial polarity and lateral organ development during evolution.

Interspecific complementation-restoration of phenotype in Arabidopsis cuc2cuc3 mutant by sugarcane CUC2 gene.

BACKGROUND: In plants, a critical balance between differentiation and proliferation of stem cells at the shoot apical meristem zone is essential for proper growth. The spatiotemporal regulation of some crucial genes dictates the formation of a boundary within and around budding organs. The boundary plays a pivotal role in distinguishing one tissue type from another and provides a defined shape to the organs at their developed stage. NAM/CUC subfamily of the NAC transcription factors control the boundary formation during meristematic development. RESULTS: Here, we have identified the CUP-SHAPED COTYLEDON (CUC) genes in sugarcane and named SsCUC2 (for the orthologous gene of CUC1 and CUC2) and SsCUC3. The phylogenetic reconstruction showed that SsCUCs occupy the CUC2 and CUC3 clade together with monocots, whereas eudicot CUC2 and CUC3 settled separately in the different clade. The structural analysis of CUC genes showed that most of the CUC3 genes were accompanied by an intron gain during eudicot divergence. Besides, the study of SsCUCs expression in the RNA-seq obtained during different stages of ovule development revealed that SsCUCs express in developing young tissues, and the expression of SsCUC2 is regulated by miR164. We also demonstrate that SsCUC2 (a monocot) could complement the cuc2cuc3 mutant phenotype of Arabidopsis (eudicot). CONCLUSIONS: This study further supports that CUC2 has diverged in CUC1 and CUC2 during the evolution of monocots and eudicots from ancestral plants. The functional analysis of CUC expression patterns during sugarcane ovule development and ectopic expression of SsCUC2 in Arabidopsis showed that SsCUC2 has a conserved role in boundary formation. Overall, these findings improve our understanding of the functions of sugarcane CUC genes. Our results reveal the crucial functional role of CUC genes in sugarcane.

TRM61 is essential for Arabidopsis embryo and endosperm development.

Post-transcriptional modifications of tRNA molecules play crucial roles in gene expression and protein biosynthesis. Across the genera, methylation of tRNAs at N1 of adenosine 58 (A58) by AtTRM61/AtTRM6 complex plays a critical role in maintaining the stability of initiator methionyl-tRNA (tRNAiMet). Recently, it was shown that mutation in AtTRM61 or AtTRM6 leads to seed abortion. However, a detailed study about the AtTRM61/AtTRM6 function in plants remains vague. Here, we found that AtTRM61 has a conserved functional structure and possesses conserved binding motifs for cofactor S-adenosyl-L-methionine (AdoMet). Mutations of the complex subunits AtTRM61/AtTRM6 result in embryo and endosperm developmental defects. The endosperm and embryo developmental defects were conditionally complemented by Attrm61-1/ + FIS2pro::AtTRM61 and Attrm61-1/ + ABI3pro::AtTRM61 indicating that AtTRM61 is required for early embryo and endosperm development. Besides, the rescue of the fertility defects in trm61/ + by overexpression of initiator tRNA suggests that AtTRM61 mutation could diminish tRNAiMet stability. Moreover, using yeast two-hybrid (Y2H) and bimolecular fluorescence complementation (BiFC) assays, we showed that AtMPK4 physically interacts with AtTRM61. The data presented here suggest that AtTRM61 has a conserved structure and function in Arabidopsis. Also, AtTRM61 may be required for tRNAiMet stability, embryo and endosperm development.

The bZIP transcription factor GmbZIP15 facilitates resistance against Sclerotinia sclerotiorum and Phytophthora sojae infection in soybean.

Soybean, one of the most valuable oilseed crops, is under constant pressure from pathogens. bZIP transcription factors (TFs) composing one of the largest TF families in plants have diverse functions. Biochemical and physiological analyses were performed to characterize the regulatory roles of soybean bZIP TF GmbZIP15 in response to pathogens. We found that transgenic soybean plants overexpressing GmbZIP15 has increased resistance against Sclerotinia sclerotiorum and Phytophthora sojae. Besides, GmbZIP15 regulates pathogen response by modulating the antioxidant defense system and phytohormone signaling. In addition, we performed chromatin immunoprecipitation sequencing to identify the downstream genes of GmbZIP15 in response to S. sclerotiorum and found that GmbZIP15 can activate or repress the expression of defense-related genes through direct promoter binding. Taken together, these results indicate that GmbZIP15 plays a positive role in pathogen resistance in soybean, and this activity may be dependent on phytohormone signaling.

The bZIP Transcription Factor GmbZIP15 Negatively Regulates Salt- and Drought-Stress Responses in Soybean.

Soybean (Glycine max), as an important oilseed crop, is constantly threatened by abiotic stress, including that caused by salinity and drought. bZIP transcription factors (TFs) are one of the largest TF families and have been shown to be associated with various environmental-stress tolerances among species; however, their function in abiotic-stress response in soybean remains poorly understood. Here, we characterized the roles of soybean transcription factor GmbZIP15 in response to abiotic stresses. The transcript level of GmbZIP15 was suppressed under salt- and drought-stress conditions. Overexpression of GmbZIP15 in soybean resulted in hypersensitivity to abiotic stress compared with wild-type (WT) plants, which was associated with lower transcript levels of stress-responsive genes involved in both abscisic acid (ABA)-dependent and ABA-independent pathways, defective stomatal aperture regulation, and reduced antioxidant enzyme activities. Furthermore, plants expressing a functional repressor form of GmbZIP15 exhibited drought-stress resistance similar to WT. RNA-seq and qRT-PCR analyses revealed that GmbZIP15 positively regulates GmSAHH1 expression and negatively regulates GmWRKY12 and GmABF1 expression in response to abiotic stress. Overall, these data indicate that GmbZIP15 functions as a negative regulator in response to salt and drought stresses.

Comparative Expression Profiling Reveals Genes Involved in Megasporogenesis.

Megasporogenesis is a key step during ovule development in angiosperms, but the small number and inaccessibility of these cells have hampered molecular and genome-wide studies. Thus, many questions remain regarding the molecular basis of cell specification, differentiation, and development in the female gametophyte. Here, taking advantage of the correlation between spikelet length and ovule development in rice (Oryza sativa), we studied the transcriptome dynamics of young ovules at three stages, the archesporial cell, the megaspore mother cell before meiosis, and the functional megaspore after meiosis, using expression profiling based on RNA sequencing. Our analysis showed that 5,274 genes were preferentially expressed in ovules during megasporogenesis as compared to ovules at the mature female gametophyte stage. Out of these, 958 (18.16%) genes were archesporial cell- and/or megaspore mother cell-preferential genes, and represent a significant enrichment of genes involved in hormone signal transduction and plant pathogen interaction pathways, as well as genes encoding transcription factors. The expression patterns of nine genes that were preferentially expressed in ovules of different developmental stages, including the OsERECTA2 (OsER2) receptor-like kinase gene, were confirmed by in situ hybridization. We further characterized the OsER2 loss-of-function mutant, which had an excessive number of female germline cells and an abnormal female gametophyte, suggesting that OsER2 regulates germline cell specification during megasporogenesis in rice. These results expand our understanding of the molecular control of megasporogenesis in rice and contribute to the functional studies of genes involved in megasporogenesis.