Dwarf and deformed flower 1, encoding an F-box protein, is critical for vegetative and floral development in rice (Oryza sativa L.)

A novel type of malformed floral organs mutant in barley was conferred by loss-of-function mutations of the MADS-box gene HvAGL6

The advanced model of floral morphogenesis is based largely on data from Arabidopsis (Arabidopsis thaliana) and rice (Oryza sativa), but this process is less well understood in the Triticeae. Here, we investigated a sterile barley (Hordeum vulgare) mutant with malformed floral organs (designated mfo1), of which the paleae, lodicules, and stamens in each floret were all converted into lemma-like organs, and the ovary was abnormally shaped. Combining bulked-segregant analysis, whole-genome resequencing, and TILLING approaches, the mfo1 mutant was attributed to loss-of-function mutations in the MADS-box transcription factor gene HvAGL6, a key regulator in the ABCDE floral morphogenesis model. Through transcriptomic analysis between young inflorescences of wild-type and mfo1 plants, 380 genes were identified as differentially expressed, most of which function in DNA binding, protein dimerization, cell differentiation, or meristem determinacy. Regulatory pathway enrichment showed HvAGL6 associates with transcriptional abundance of many MADS-box genes, including the B-class gene HvMADS4. Mutants with deficiency in HvMADS4 exhibited the conversion of stamens into supernumerary pistils, producing multiple ovaries resembling the completely sterile multiple ovaries 3.h (mov3.h) mutant. These findings demonstrate that the regulatory model of floral morphogenesis is conserved across plant species and provides insights into the interactions between HvAGL6 and other MADS-box regulators.

Comprehensive identification and analysis of DUF640 genes associated with rice growth

Protein domains with conserved amino acid sequences and uncharacterized functions are called domains of unknown function (DUF). The DUF640 gene family plays a crucial role in plant growth, particularly in light regulation, floral organ development, and fruit development. However, there exists a lack of systematic understanding of the evolutionary relationships and functional differentiation of DUF640 within the Oryza genus. In this study, 61 DUF640 genes were identified in the Oryza genus. The expression of DUF640s is induced by multiple hormonal stressors including abscisic acid (ABA), cytokinin (CK), ethylene (ETH), and indole-3-acetic acid (IAA). Specifically, OiDUF640-10 expression significantly increased after ETH treatment. Transgenic experiments showed that overexpressing OiDUF640-10 lines were sensitive to ETH, and seedling length was obstructed. Evolutionary analysis revealed differentiation of the OiDUF640-10 gene in O. sativa ssp. indica and japonica varieties, likely driven by natural selection during the domestication of cultivated rice. These results indicate that OiDUF640-10 plays a vital role in the regulation of rice seedling length.

Genome-wide identification and characterization of AP2/ERF gene superfamily during flower development in Actinidia eriantha

Background

As one of the largest transcription factor families in plants, AP2/ERF gene superfamily plays important roles in plant growth, development, fruit ripening and biotic and abiotic stress responses. Despite the great progress has been made in kiwifruit genomic studies, little research has been conducted on the AP2/ERF genes of kiwifruit. The increasing kiwifruit genome resources allowed us to reveal the tissue expression profiles of AP2/ERF genes in kiwifruit on a genome-wide basis.

Results

In present study, a total of 158 AP2/ERF genes in A. eriantha were identified. All genes can be mapped on the 29 chromosomes. Phylogenetic analysis divided them into four main subfamilies based on the complete protein sequences. Additionally, our results revealed that the same subfamilies contained similar gene structures and conserved motifs. Ka/Ks calculation indicated that AP2/ERF gene family was undergoing a strong purifying selection and the evolutionary rates were slow. RNA-seq showed that the AP2/ERF genes were expressed differently in different flower development stages and 56 genes were considered as DEGs among three contrasts. Moreover, qRT-PCR suggested partial genes showed significant expressions as well, suggesting they could be key regulators in flower development in A. eriantha. In addition, two genes (AeAP2/ERF061, AeAP2/ERF067) had abundant transcription level based on transcriptomes, implying that they may play a crucial role in plant flower development regulation and flower tissue forming.

Conclusions

We identified AP2/ERF genes and demonstrated their gene structures, conserved motifs, and phylogeny relationships of AP2/ERF genes in two related species of kiwifruit, A. eriantha and A. chinensis, and their potential roles in flower development in A. eriantha. Such information would lay the foundation for further functional identification of AP2/ERF genes involved in kiwifruit flower development.

Supplementary Information

The online version contains supplementary material available at 10.1186/s12864-022-08871-4.

Du13 encodes a C2 H2 zinc-finger protein that regulates Wxb pre-mRNA splicing and microRNA biogenesis in rice endosperm

Amylose content is a crucial physicochemical property responsible for the eating and cooking quality of rice (Oryza sativa L.) grain and is mainly controlled by the Waxy (Wx) gene. Previous studies have identified several Dull genes that modulate the expression of the Wx^b allele in japonica rice by affecting the splicing efficiency of the Wx^b pre-mRNA. Here, we uncover dual roles for a novel Dull gene in pre-mRNA splicing and microRNA processing. We isolated the dull mutant, du13, with a dull endosperm and low amylose content. Map-based cloning showed that Du13 encodes a C₂ H₂ zinc-finger protein. Du13 coordinates with the nuclear cap-binding complex to regulate the splicing of Wx^b transcripts in rice endosperm. Moreover, Du13 also regulates alternative splicing of other protein-coding transcripts and affects the biogenesis of a subset of microRNAs. Our results reveal an evolutionarily conserved link between pre-mRNA splicing and microRNA biogenesis in rice endosperm. Our findings also provide new insights into the functions of Dull genes in rice and expand our knowledge of microRNA biogenesis in monocots.

Transcriptome profiling of two super hybrid rice provides insights into the genetic basis of heterosis

BACKGROUND

Heterosis is a phenomenon that hybrids show superior performance over their parents. The successful utilization of heterosis has greatly improved rice productivity, but the molecular basis of heterosis remains largely unclear.

RESULTS

Here, the transcriptomes of young panicles and leaves of the two widely grown two-line super hybrid rice varieties (Jing-Liang-You-Hua-Zhan (JLYHZ) and Long-Liang-You-Hua-Zhan (LLYHZ)) and their parents were analyzed by RNA-seq. Transcriptome profiling of the hybrids revealed 1,778 ~ 9,404 differentially expressed genes (DEGs) in two tissues, which were identified by comparing with their parents. GO, and KEGG enrichment analysis showed that the pathways significantly enriched in both tissues of two hybrids were all related to yield and resistance, like circadian rhythm (GO:0,007,623), response to water deprivation (GO:0,009,414), and photosynthetic genes (osa00196). Allele-specific expression genes (ASEGs) were also identified in hybrids. The ASEGs were most significantly enriched in ionotropic glutamate receptor signaling pathway, which was hypothesized to be potential amino acid sensors in plants. Moreover, the ASEGs were also differentially expressed between parents. The number of variations in ASEGs is higher than expected, especially for large effect variations. The DEGs and ASEGs are the potential reasons for the formation of heterosis in the two elite super hybrid rice.

CONCLUSIONS

Our results provide a comprehensive understanding of the heterosis of two-line super hybrid rice and facilitate the exploitation of heterosis in hybrid rice breeding with high yield heterosis.

The 14-3-3 protein GF14c positively regulates immunity by modulating the protein homoeostasis of the GRAS protein OsSCL7 in rice

Various types of transcription factors have been reported to be involved in plant-pathogen interactions by regulating defence-related genes. GRAS proteins, plant- specific transcription factors, have been shown to play essential roles in plant growth, development and stress responses. By performing a transcriptome study on rice early defence responses to Magnaporthe oryzae, we identified a GRAS protein, OsSCL7, which was induced by M. oryzae infection. We characterized the function of OsSCL7 in rice disease resistance. OsSCL7 was upregulated upon exposure to M. oryzae and pathogen-associated molecular pattern treatments, and knocking out OsSCL7 resulted in decreased disease resistance of rice to M. oryzae. In contrast, overexpression of OsSCL7 could improve rice disease resistance to M. oryzae. OsSCL7 was mainly localized in the nucleus and showed transcriptional activity. OsSCL7 can interact with GF14c, a 14-3-3 protein, and loss-of-function GF14c leads to enhanced susceptibility to M. oryzae. Additionally, OsSCL7 protein levels were reduced in the gf14c mutant and knocking out OsSCL7 affected the expression of a series of defence-related genes. Taken together, these findings uncover the important roles of OsSCL7 and GF14c in plant immunity and a potential mechanism by which plants fine-tune immunity by regulating the protein stability of a GRAS protein via a 14-3-3 protein.

Overexpression of Liriodendron tulipifera JAG Gene (LtuJAG) Changes Leaf Shapes in Transgenic Arabidopsis thaliana

In Arabidopsis thaliana, JAGGED (JAG) is a transcription inhibitor that controls the development of leaf polarity and regulates the expression of genes controlling lateral organ formation. Liriodendron tulipifera is an ornamental tree with extraordinary tulip-shaped flowers and goose web-like leaves, this is one of the suitable plants for morphological development research. To investigate the potential functions of the LtuJAG gene, we isolated the full-length LtuJAG from L. tulipifera, transferred it into A. thaliana via agrobacterium-mediated transformation, and monitored its expression pattern. Subcellular localization showed that LtuJAG was located in the nucleus. RT-qPCR assays indicated that LtuJAG was expressed mainly in leaf buds and flowers, but not in mature leaves and stems. GUS staining results showed that LtuJAG was expressed in the shoot apical meristem (SAM). Overexpressing LtuJAG changed A. thaliana leaf shapes, causing a moderate serration and a slight asymmetric distribution in the medio-lateral and proximal-distal axes. Ectopic expression of LtuJAG induced the expression of lateral organ boundary suppressors JAGGED LATERAL ORGANS (JLO) and ARABIDOPSIS THALIANA HOMEOBOX1 (ATH1). It also repressed the expression of the apical meristem suppressor class-1 KNOX gene (KNOX I) and altered endogenous hormone levels. Our results suggest that LtuJAG plays a role in negatively regulating leaf polarity formation in L. tulipifera.

Separable regulation of POW1 in grain size and leaf angle development in rice

Leaf angle is one of the key factors that determines rice plant architecture. However, the improvement of leaf angle erectness is often accompanied by unfavourable changes in other traits, especially grain size reduction. In this study, we identified the pow1 (put on weight 1) mutant that leads to increased grain size and leaf angle, typical brassinosteroid (BR)-related phenotypes caused by excessive cell proliferation and cell expansion. We show that modulation of the BR biosynthesis genes OsDWARF4 (D4) and D11 and the BR signalling gene D61 could rescue the phenotype of leaf angle but not grain size in the pow1 mutant. We further demonstrated that POW1 functions in grain size regulation by repressing the transactivation activity of the interacting protein TAF2, a highly conserved member of the TFIID transcription initiation complex. Down-regulation of TAF2 rescued the enlarged grain size of pow1 but had little effect on the increased leaf angle phenotype of the mutant. The separable functions of the POW1-TAF2 and POW1-BR modules in grain size and leaf angle control provide a promising strategy for designing varieties with compact plant architecture and increased grain size, thus promoting high-yield breeding in rice.

HvLEAFY controls the early stages of floral organ specification and inhibits the formation of multiple ovaries in barley

Transition to the reproductive phase, inflorescence formation and flower development are crucial elements that ensure maximum reproductive success in a plant's life cycle. To understand the regulatory mechanisms underlying correct flower development in barley (Hordeum vulgare), we characterized the multiovary 5 (mov5.o) mutant. This mutant develops abnormal flowers that exhibit mosaic floral organs typified by multiple carpels at the total or partial expense of stamens. Genetic mapping positioned mov5 on the long arm of chromosome 2H, incorporating a region that encodes HvLFY, the barley orthologue of LEAFY from Arabidopsis. Sequencing revealed that, in mov5.o plants, HvLFY contains a single amino acid substitution in a highly conserved proline residue. CRISPR-mediated knockout of HvLFY replicated the mov5.o phenotype, suggesting that HvLFY_mov5 represents a loss of function allele. In heterologous assays, the HvLFY_mov5 polymorphism influenced protein-protein interactions and affinity for a putative binding site in the promoter of HvMADS58, a C-class MADS-box gene. Moreover, molecular analysis indicated that HvLFY interacts with HvUFO and regulates the expression of floral homeotic genes including HvMADS2, HvMADS4 and HvMADS16. Other distinct changes in expression differ from those reported in the rice LFY mutants apo2/rfl, suggesting that LFY function in the grasses is modulated in a species-specific manner. This pathway provides a key entry point for the study of LFY function and multiple ovary formation in barley, as well as cereal species in general.

Genetic Diversity Relationship Between Grain Quality and Appearance in Rice

Grain quality is an important breeding objective in rice, and the appearance of the grain also affects its commercial value in the market. The aim of this study was to decode the rice grain qualities and appearances, such as gelatinization temperature (GT), amylose content (AC), grain protein content (GPC), pericarp color (PC), length/width ratio (LWR), and grain volume (GV) at phenotypic and genetic levels, as well as the relationships among them. A genome-wide association study (GWAS) was used to identify the quantitative trait locus (QTLs) associated with the target traits using mixed linear model (MLM) and Bayesian-information and linkage-disequilibrium iteratively nested keyway (BLINK) methods. In general, AC was negatively correlated with GPC and GV, while it was positively correlated with LWR and PC. GPC was positively correlated with LWR. Using the rice diversity panel 1 (RDP1) population, we identified 11, 6, 2, 7, 11, and 6 QTLs associated with GT, AC, GPC, PC, LWR, and GV, respectively. Five germplasm lines, superior in grain qualities and appearances for basic breeding materials or improvement, were identified. Notably, an F-box gene OsFbox394 was located in the linkage disequilibrium (LD) block of qLWR7-2, which specifically expresses in endosperm and seed tissues, suggesting that this gene may regulate the seed development in rice grain. Besides, different haplotypes of OsHyPRP45 showed significant differences in AC, indicating that this gene may be related to AC in rice grain.

Mapping a Partial Andromonoecy Locus in Citrullus lanatus Using BSA-Seq and GWAS Approaches

The sexual expression of watermelon plants is the result of the distribution and occurrence of male, female, bisexual and hermaphrodite flowers on the main and secondary stems. Plants can be monoecious (producing male and female flowers), andromonoecious (producing male and hermaphrodite flowers), or partially andromonoecious (producing male, female, bisexual, and hermaphrodite flowers) within the same plant. Sex determination of individual floral buds and the distribution of the different flower types on the plant, are both controlled by ethylene. A single missense mutation in the ethylene biosynthesis gene CitACS4, is able to promote the conversion of female into hermaphrodite flowers, and therefore of monoecy (genotype MM) into partial andromonoecy (genotype Mm) or andromonoecy (genotype mm). We phenotyped and genotyped, for the M/m locus, a panel of 207 C. lanatus accessions, including five inbreds and hybrids, and found several accessions that were repeatedly phenotyped as PA (partially andromonoecious) in several locations and different years, despite being MM. A cosegregation analysis between a SNV in CitACS4 and the PA phenotype, demonstrated that the occurrence of bisexual and hermaphrodite flowers in a PA line is not dependent on CitACS4, but conferred by an unlinked recessive gene which we called pa. Two different approaches were performed to map the pa gene in the genome of C. lanatus: bulk segregant analysis sequencing (BSA-seq) and genome wide association analysis studies (GWAS). The BSA-seq study was performed using two contrasting bulks, the monoecious M-bulk and the partially andromonoecious PA-bulk, each one generated by pooling DNA from 20 F2 plants. For GWAS, 122 accessions from USDA gene bank, already re-sequenced by genotyping by sequencing (GBS), were used. The combination of the two approaches indicates that pa maps onto a genomic region expanding across 32.24-36.44 Mb in chromosome 1 of watermelon. Fine mapping narrowed down the pa locus to a 867 Kb genomic region containing 101 genes. A number of candidate genes were selected, not only for their function in ethylene biosynthesis and signalling as well as their role in flower development and sex determination, but also by the impact of the SNPs and indels differentially detected in the two sequenced bulks.

Identify QTLs and candidate genes underlying source-, sink-, and grain yield-related traits in rice by integrated analysis of bi-parental and natural populations

The source-sink relationship determines the ultimate grain yield of rice. In this study, we used a set of reciprocal introgression lines (ILs) derived from Xuishui09 × IR2061 to map quantitative trait loci (QTLs) that were associated with sink-, source-, and grain yield-related traits. A total of 95 QTLs influencing eight measured traits were identified using 6181 high-quality single nucleotide polymorphism markers. Nine background-independent QTLs were consistently detected in seven chromosomal regions in different genetic backgrounds. Seven QTLs clusters simultaneously affected sink-, source-, and grain yield-related traits, probably due to the genetic basis of significant correlations of grain yield with source and sink traits. We selected 15 candidate genes in the four QTLs consistently identified in the two populations by performing gene-based association and haplotype analyses using 2288 accessions from the 3K project. Among these, LOC_Os03g48970 for qTSN3b, LOC_Os06g04710 for qFLL6a, and LOC_Os07g32510 for qTGW7 were considered as the most likely candidate genes based on functional annotations. These results provide a basis for further study of candidate genes and for the development of high-yield rice varieties by balancing source–sink relationships using marker-assisted selection.

Hybrid breeding in wheat: how shaping floral biology can offer new perspectives

Hybrid breeding in wheat (Triticum aestivum L.) has the potential to deliver major yield increases. This is a requisite to guarantee food security for increasing population demands and to counterbalance the effects of extreme environmental conditions. Successful hybrid breeding in wheat relies on forced outcrossing while preventing self-pollination. To achieve this, research has been directed towards identifying and improving fertility control systems. To maximise cross-pollination and seed set, however, fertility control systems need to be complemented by breeding phenotypically distinct male and female lines. This review summarises existing and novel male sterility systems for wheat hybridisation. We also consider the genetic resources that can be used to alter wheat's floral development and spike morphology, with a focus on the genetic variation already available. Exploiting these resources can lead to enhanced outcrossing, a key requirement in the progress towards hybrid wheat breeding.

Identification and characterization of the stunted sterile (ss) mutant in rice

BACKGROUND

Proper organ development is pivotal for normal rice growth and production. Many genes are involved in this process, and these genes provide a basis for rice breeding.

OBJECTIVE

To identify a novel mutation causing developmental defects in rice.

METHODS

The phenotype of a rice mutant, stunted sterile (ss), identified from the japonica rice cultivar Samkwang treated with N-methyl-N-nitrosourea, was characterized, including anatomical and pollen activity analyses. A genetic analysis and fine mapping were performed to identify a candidate locus, followed by a sequence analysis to determine the causal mutation for the phenotype.

RESULTS

Compared with wild-type plants, the mutant exhibited a 34% reduction in height, 46% reduction in flag leaf width, and complete panicle sterility. Cell proliferation in the leaf and pollen viability were significantly inhibited in the mutant. The mutant phenotypes were controlled by a single recessive gene that was fine-mapped to an 84 kb region between two SNP markers on the short arm of chromosome 5. A candidate gene analysis determined that the mutant carries an 11 bp insertion in the coding region of LOC_Os05g03550, which encodes a protein containing two SANT domains, resulting in a premature termination codon before the conserved domain.

CONCLUSIONS

We identified a novel rice gene, Stunted sterile, involved in the regulation of various developmental processes. Our findings improve our understanding of the role of chromatin remodeling in organ development and have implications for breeding owing to the broad effects of the gene on plant growth.

Genome wide screening and comparative genome analysis for Meta-QTLs, ortho-MQTLs and candidate genes controlling yield and yield-related traits in rice

Background

Improving yield and yield-related traits is the crucial goal in breeding programmes of cereals. Meta-QTL (MQTL) analysis discovers the most stable QTLs regardless of populations genetic background and field trial conditions and effectively narrows down the confidence interval (CI) for identification of candidate genes (CG) and markers development.

Results

A comprehensive MQTL analysis was implemented on 1052 QTLs reported for yield (YLD), grain weight (GW), heading date (HD), plant height (PH) and tiller number (TN) in 122 rice populations evaluated under normal condition from 1996 to 2019. Consequently, these QTLs were confined into 114 MQTLs and the average CI was reduced up to 3.5 folds in compare to the mean CI of the original QTLs with an average of 4.85 cM CI in the resulted MQTLs. Among them, 27 MQTLs with at least five initial QTLs from independent studies were considered as the most stable QTLs over different field trials and genetic backgrounds. Furthermore, several known and novel CGs were detected in the high confident MQTLs intervals. The genomic distribution of MQTLs indicated the highest density at subtelomeric chromosomal regions. Using the advantage of synteny and comparative genomics analysis, 11 and 15 ortho-MQTLs were identified at co-linear regions between rice with barley and maize, respectively. In addition, comparing resulted MQTLs with GWAS studies led to identification of eighteen common significant chromosomal regions controlling the evaluated traits.

Conclusion

This comprehensive analysis defines a genome wide landscape on the most stable loci associated with reliable genetic markers and CGs for yield and yield-related traits in rice. Our findings showed that some of these information are transferable to other cereals that lead to improvement of their breeding programs.

Diverse and dynamic roles of F-box proteins in plant biology

The SCF complex is a widely studied multi-subunit ring E3 ubiquitin ligase that tags targeted proteins with ubiquitin for protein degradation by the ubiquitin 26S-proteasome system (UPS). The UPS is an important system that generally keeps cellular events tightly regulated by purging misfolded or damaged proteins and selectively degrading important regulatory proteins. The specificity of this post-translational regulation is controlled by F-box proteins (FBPs) via selective recognition of a protein-protein interaction motif at the C-terminal domain. Hence, FBPs are pivotal proteins in determining the plant response in multiple scenarios. It is not surprising that the FBP family is one of the largest protein families in the plant kingdom. In this review, the roles of FBPs, specifically in plants, are compiled to provide insights into their involvement in secondary metabolites, plant stresses, phytohormone signalling, plant developmental processes and miRNA biogenesis.

A 3-bp deletion of WLS5 gene leads to weak growth and early leaf senescence in rice

BACKGROUND

In rice (Oryza sativa) and other grains, weak growth (dwarfism, short panicle length, and low seed-setting rate) and early senescence lead to reduced yield. The molecular mechanisms behind these processes have been widely studied; however, the complex genetic regulatory networks controlling growth and senescence require further elucidation.

RESULTS

We isolated a mutant exhibiting weak growth throughout development and early senescence of leaf tips, and designated this mutant weakness and leaf senescence5 (wls5). Histological analysis showed that the poor growth of wls5 plants involved a reduction in cell length and number. Physiological analysis and transmission electron microscopy revealed that the wls5 cells had abnormal chloroplasts, and the mutants underwent chlorophyll degradation triggered by accumulation of reactive oxygen species. Consistent with this, RNA sequencing revealed changes in senescence-related gene expression in wls5 plants. The wls5 mutants also exhibited significantly higher stomatal density and altered phytohormone contents compared with wild-type plants. Fine mapping delimited WLS5 to a 29-kb region on chromosome 5. DNA sequencing of wls5 identified a 3-bp deletion in the first exon of LOC_Os05g04900, resulting in a deletion of a lysine in the predicted protein. Knockout of LOC_Os05g04900 in Nipponbare plants caused leaf senescence, confirming this locus as the causal gene for WLS5.

CONCLUSIONS

We identified a novel mutant (wls5) that affects plant development and leaf senescence in rice. LOC_Os05g04900, encoding a protein of unknown function, is the causal gene for wls5. Further molecular study of WLS5 will uncover the roles of this gene in plant growth and leaf senescence.

Regulation of meristem maintenance and organ identity during rice reproductive development

Grasses have evolved complex inflorescences, where the primary unit is the specialized short branch called a spikelet. Detailed studies of the cumulative action of the genetic regulators that direct the progressive change in axillary meristem identity and their terminal differentiation are crucial to understanding the complexities of the inflorescence and the development of a determinate floret. Grass florets also pose interesting questions concerning the morphologies and functions of organs as compared to other monocots and eudicots. In this review, we summarize our current knowledge of the regulation of the transitions that occur in grass inflorescence meristems, and of the specification of floret meristems and their determinate development. We primarily use rice as a model, with appropriate comparisons to other crop models and to the extensively studied eudicot Arabidopsis. The role of MADS-domain transcription factors in floral organ patterning is well documented in many eudicots and in grasses. However, there is evidence to suggest that some of these rice floral regulators have evolved distinctive functions and that other grass species-specific factors and regulatory pathways occur - for example the LOFSEP 'E' class genes OsMADS1 and OsMAD34, and ramosa genes. A better understanding of these systems and the epigenetic regulators and hormone signaling pathways that interact with them will provide new insights into the rice inflorescence meristem and the differentiation of its floret organs, and should indicate genetic tools that can be used to control yield-related traits in both rice and other cereal crops.

Genome-wide dynamic network analysis reveals a critical transition state of flower development in Arabidopsis

BACKGROUND

The flowering transition which is controlled by a complex and intricate gene regulatory network plays an important role in the reproduction for offspring of plants. It is a challenge to identify the critical transition state as well as the genes that control the transition of flower development. With the emergence of massively parallel sequencing, a great number of time-course transcriptome data greatly facilitate the exploration of the developmental phase transition in plants. Although some network-based bioinformatics analyses attempted to identify the genes that control the phase transition, they generally overlooked the dynamics of regulation and resulted in unreliable results. In addition, the results of these methods cannot be self-explained.

RESULTS

In this work, to reveal a critical transition state and identify the transition-specific genes of flower development, we implemented a genome-wide dynamic network analysis on temporal gene expression data in Arabidopsis by dynamic network biomarker (DNB) method. In the analysis, DNB model which can exploit collective fluctuations and correlations of different metabolites at a network level was used to detect the imminent critical transition state or the tipping point. The genes that control the phase transition can be identified by the difference of weighted correlations between the genes interested and the other genes in the global network. To construct the gene regulatory network controlling the flowering transition, we applied NARROMI algorithm which can reduce the noisy, redundant and indirect regulations on the expression data of the transition-specific genes. In the results, the critical transition state detected during the formation of flowers corresponded to the development of flowering on the 7th to 9th day in Arabidopsis. Among of 233 genes identified to be highly fluctuated at the transition state, a high percentage of genes with maximum expression in pollen was detected, and 24 genes were validated to participate in stress reaction process, as well as other floral-related pathways. Composed of three major subnetworks, a gene regulatory network with 150 nodes and 225 edges was found to be highly correlated with flowering transition. The gene ontology (GO) annotation of pathway enrichment analysis revealed that the identified genes are enriched in the catalytic activity, metabolic process and cellular process.

CONCLUSIONS

This study provides a novel insight to identify the real causality of the phase transition with genome-wide dynamic network analysis.

GmSK1, an SKP1 homologue in soybean, is involved in the tolerance to salt and drought

In plants, various proteins are regulated by the ubiquitin-mediated system in response to different environmental stresses, such as drought, cold and heat. The Skp1-Cullin-F-box (SCF) complex, one of the multisubunit E3 ligases, has been shown to be involved in abiotic response pathways. In this study, Glycine max SKP1-like 1 (GmSK1), which had the typical characteristics of an SKP1 protein, with an alpha/beta structure, targeted to the cytoplasm and nucleus, was isolated from soybean [Glycine max (L.)]. GmSK1 was constitutively expressed in all the tested tissues, especially in the roots. Furthermore, the expression of GmSK1 was simultaneously induced by abscisic acid (ABA), jasmonic acid (JA), salicylic acid (SA), NaCl, low temperatures and drought, which suggests important roles for GmSK1 in plant responses to hormone treatments and abiotic stress. GmSK1-overexpressing transgenic tobacco (Nicotiana tobacum cv. Samsun) plants showed enhanced tolerance to high salinity and drought stress; exhibited significantly reduced inhibition of growth, greenness and water loss; and exhibited increased MDA accumulation compared with wild-type controls. Our results suggest that GmSK1 might play a role in the crosstalk between ubiquitination and abiotic stress responses in plants.

Next-generation sequencing from bulked segregant analysis identifies a dwarfism gene in watermelon

Dwarfism is one of the most valuable traits in watermelon breeding mainly because of its contribution to yield as well as the decreased labor required to cultivate and harvest smaller plants. However, the underlying genetic mechanism is unknown. In this study, a candidate dwarfism gene was identified by applying next-generation sequencing technology to analyze watermelon plants. We completed a whole-genome re-sequencing of two DNA bulks (dwarf pool and vine pool) generated from plants in an F₂ population. A genome-wide analysis of single nucleotide polymorphisms resulted in the detection of a genomic region harboring the candidate dwarfism gene Cla010726. The encoded protein was predicted to be a gibberellin 20-oxidase-like protein, which is a well-known “green revolution” protein in other crops. A quantitative real-time PCR investigation revealed that the Cla010726 expression level was significantly lower in the dwarf plants than in the normal-sized plants. The SNP analysis resulted in two SNP locating in the Cla010726 gene promoter of dsh F₂ individuals. The results presented herein provide preliminary evidence that Cla010726 is a possible dwarfism gene.

Fine Mapping of a Novel defective glume 1 (dg1) Mutant, Which Affects Vegetative and Spikelet Development in Rice

In cereal crops, vegetative and spikelet development play important roles in grain yield and quality, but the genetic mechanisms that control vegetative and spikelet development remain poorly understood in rice. Here, we identified a new rice mutant, defective glume 1 (dg1) mutant from cultivar Zhonghua11 after ethyl methanesulfonate treatment. The dg1 mutant displayed the dwarfism with small, rolled leaves, which resulted from smaller cells and more bulliform cells. The dg1 mutant also had an enlarged leaf angle and defects in brassinosteroid signaling. In the dg1 mutant, both the rudimentary glume and sterile lemma (glumes) were transformed into lemma-like organ and acquired the lemma identity. Additionally, the dg1 mutant produced slender grains. Further analysis revealed that DG1 affects grain size by regulating cell proliferation and expansion. We fine mapped the dg1 locus to a 31-kb region that includes eight open reading frames. We examined the DNA sequence and expression of these loci, but we were not able to identify the DG1 gene. Therefore, more work will be needed for cloning and functional analysis of DG1, which would contribute to our understanding of the molecular mechanisms behind whole-plant development in rice.

Polycomb Protein OsFIE2 Affects Plant Height and Grain Yield in Rice

Polycomb group (PcG) proteins have been shown to affect growth and development in plants. To further elucidate their role in these processes in rice, we isolated and characterized a rice mutant which exhibits dwarfism, reduced seed setting rate, defective floral organ, and small grains. Map-based cloning revealed that abnormal phenotypes were attributed to a mutation of the Fertilization Independent Endosperm 2 (OsFIE2) protein, which belongs to the PcG protein family. So we named the mutant as osfie2-1. Histological analysis revealed that the number of longitudinal cells in the internodes decreased in osfie2-1, and that lateral cell layer of the internodes was markedly thinner than wild-type. In addition, compared to wild-type, the number of large and small vascular bundles decreased in osfie2-1, as well as cell number and cell size in spikelet hulls. OsFIE2 is expressed in most tissues and the coded protein localizes in both nucleus and cytoplasm. Yeast two-hybrid and bimolecular fluorescence complementation assays demonstrated that OsFIE2 interacts with OsiEZ1 which encodes an enhancer of zeste protein previously identified as a histone methylation enzyme. RNA sequencing-based transcriptome profiling and qRT-PCR analysis revealed that some homeotic genes and genes involved in endosperm starch synthesis, cell division/expansion and hormone synthesis and signaling are differentially expressed between osfie2-1 and wild-type. In addition, the contents of IAA, GA3, ABA, JA and SA in osfie2-1 are significantly different from those in wild-type. Taken together, these results indicate that OsFIE2 plays an important role in the regulation of plant height and grain yield in rice.

The pleiotropic ABNORMAL FLOWER AND DWARF1 affects plant height, floral development and grain yield in rice

Moderate plant height and successful establishment of reproductive organs play pivotal roles in rice grain production. The molecular mechanism that controls the two aspects remains unclear in rice. In the present study, we characterized a rice gene, ABNORMAL FLOWER AND DWARF1 (AFD1) that determined plant height, floral development and grain yield. The afd1 mutant showed variable defects including the dwarfism, long panicle, low seed setting and reduced grain yield. In addition, abnormal floral organs were also observed in the afd1 mutant including slender and thick hulls, and hull-like lodicules. AFD1 encoded a DUF640 domain protein and was expressed in all tested tissues and organs. Subcellular localization showed AFD1-green fluorescent fusion protein (GFP) was localized in the nucleus. Meantime, our results suggested that AFD1 regulated the expression of cell division and expansion related genes.

Genome-wide survey and expression analysis of F-box genes in chickpea

BACKGROUND

The F-box genes constitute one of the largest gene families in plants involved in degradation of cellular proteins. F-box proteins can recognize a wide array of substrates and regulate many important biological processes such as embryogenesis, floral development, plant growth and development, biotic and abiotic stress, hormonal responses and senescence, among others. However, little is known about the F-box genes in the important legume crop, chickpea. The available draft genome sequence of chickpea allowed us to conduct a genome-wide survey of the F-box gene family in chickpea.

RESULTS

A total of 285 F-box genes were identified in chickpea which were classified based on their C-terminal domain structures into 10 subfamilies. Thirteen putative novel motifs were also identified in F-box proteins with no known functional domain at their C-termini. The F-box genes were physically mapped on the 8 chickpea chromosomes and duplication events were investigated which revealed that the F-box gene family expanded largely due to tandem duplications. Phylogenetic analysis classified the chickpea F-box genes into 9 clusters. Also, maximum syntenic relationship was observed with soybean followed by Medicago truncatula, Lotus japonicus and Arabidopsis. Digital expression analysis of F-box genes in various chickpea tissues as well as under abiotic stress conditions utilizing the available chickpea transcriptome data revealed differential expression patterns with several F-box genes specifically expressing in each tissue, few of which were validated by using quantitative real-time PCR.

CONCLUSIONS

The genome-wide analysis of chickpea F-box genes provides new opportunities for characterization of candidate F-box genes and elucidation of their function in growth, development and stress responses for utilization in chickpea improvement.