Regulation Of Flower Development Research Articles

Molecular characterization of SPL gene family during flower morphogenesis and regulation in blueberry

The SPL gene is a plant-specific transcription factor involved in the regulation of plant growth and development, which have been identified in woody plants. The process of floral bud differentiation affects the timing of flowering and fruit set and regulates plant growth, however, the mechanism of regulation of flower development by SPL genes is less studied. In this study, 56 VcSPL genes were identified in the tetraploid blueberry. The VcSPL gene family was classified into six subfamilies, and analysis of cis-elements showed that VcSPL genes were regulated by light, phytohormones (abscisic acid, MeJA), and low temperature. In the evolutionary analysis, segmental replication may play an important role in VcSPL gene amplification. Interestingly, we also studied diploid blueberry (Bilberry), in which 24 SPL genes were identified, and 36 homologous pairs were found, suggesting a high degree of convergence in the syntenic relationship between blueberry (Vaccinium corymbosum L) and bilberry (Vaccinium darrowii). Based on the expression profile, VcSPL genes were expressed at high levels in flowers, shoots, and roots, indicating a diversity of gene functions. Then we selected 20 differentially-expressed SPL genes to further investigate the role of VcSPL in floral induction and initiation. It showed that the genes VcSPL40, VcSPL35, VcSPL45, and VcSPL53 may play a crucial role in the blueberry floral transition phase (from vegetative growth to flower initiation). These results provided important information for understanding and exploring the role of VcSPLs in flower morphogenesis and plant growth.

Integrated cytological and transcriptomic analysis reveals insights into pollen fertility in newly synthetic Brassica allohexaploids.

Trigenomic Brassica allohexaploids (AABBCC, 2n = 6x = 54) have great potential in oilseed breeding and genetic diversity. However, Brassica allohexaploids do not exist naturally, and the underlying mechanism regulating pollen fertility in artificially synthesized Brassica allohexaploids is still unclear. In this study, synthetic Brassica allohexaploids were produced by crossing allotetraploid B. carinata (BBCC, 2n = 4x = 34) and diploid B. rapa (AA, 2n = 2x = 20), followed by chromosome doubling. The results showed that the pollen fertility was significantly reduced and the pollen structures were mostly distorted, but the nursing anther tapetum developed normally in the synthetic Brassica allohexaploids. Furthermore, the data showed that the meiotic events occurred irregularly with uneven chromosome segregation and microspore development appeared mostly abnormal. Transcription analysis showed that the upregulation of genes related to the negative regulation of flower development and the downregulation of genes related to chromosome segregation might play an essential role in reduction of pollen fertility in the Brassica allohexaploids. In conclusion, this study elucidated the related mechanisms affecting pollen fertility during male gametophytic development at the cytological and transcriptomic levels in the newly synthesized Brassica allohexaploids.

B Class Floral Homeotic Genes are Involved in the Petal Identity and Flower Meristem Determinations in Chrysanthemum morifolium

Chrysanthemum morifolium, an ornamental crop with diverse forms of inflorescence, is a good model for studying flower development in Asteraceae. However, the genetic background is complex and the mechanisms of regulating flower development are still unclear. Here, we identified two natural mutant lines of chrysanthemum and named them M1 and M2 according to the severity of the phenotype. Both lines showed defects in petal identity, and the petals of the M1 line had a mild phenotype: partially loss of petal identity and conversion of petals into green, leaf-like organs. The M2 line had severe phenotypes: in addition to severe petal defects, secondary inflorescences were produced in the capitulum to replace the normal ray and disc florets, which indicated a transformation of a flower meristem into an inflorescence meristem. Transcriptome sequencing of WT and M2 inflorescences was performed and found altered expression of floral organ development A, B and E class genes, where B and E class genes were significantly down-regulated. qRT-PCR analysis in both M1 and M2 lines revealed that the expression of three chrysanthemum class B genes CmAP3.1, CmAP3.2 and CmPI, was negatively correlated with phenotypic severity. This suggests that class B genes in chrysanthemum not only have conserved functions in determining petal identity but also were involved in the determinacy of the flower meristem. This study provides insights into the functions of class B genes in flower development, and is informative for dissecting the molecular mechanisms of flower development in chrysanthemum.

The role of CDPKs in plant development, nutrient and stress signaling.

The second messenger calcium (Ca2+) is a ubiquitous intracellular signaling molecule found in eukaryotic cells. In plants, the multigene family of calcium-dependent protein kinases (CDPKs) plays an important role in regulating plant growth, development, and stress tolerance. CDPKs sense changes in intracellular Ca2+ concentration and translate them into phosphorylation events that initiate downstream signaling processes. Several functional and expression studies on different CDPKs and their encoding genes have confirmed their multifunctional role in stress. Here, we provide an overview of the signal transduction mechanisms and functional roles of CDPKs. This review includes details on the regulation of secondary metabolites, nutrient uptake, regulation of flower development, hormonal regulation, and biotic and abiotic stress responses.

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

BackgroundAs 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.ResultsIn 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.ConclusionsWe 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.

Transcriptome Analysis to Identify Genes Related to Flowering Reversion in Tomato.

Flowering reversion is a common phenomenon in plant development in which differentiated floral organs switch from reproductive growth to vegetative growth and ultimately form abnormal floral organs or vegetative organs. This greatly reduces tomato yield and quality. Research on this phenomenon has recently increased, but there is a lack of research at the molecular and gene expression levels. Here, transcriptomic analyses of the inflorescence meristem were performed in two kinds of materials at different developmental stages, and a total of 3223 differentially expressed genes (DEGs) were screened according to the different developmental stages and trajectories of the two materials. The analysis of database annotations showed that these DEGs were closely related to starch and sucrose metabolism, DNA replication and modification, plant hormone synthesis and signal transduction. It was further speculated that tomato flowering reversion may be related to various biological processes, such as cell signal transduction, energy metabolism and protein post-transcriptional regulation. Combined with the results of previous studies, our work showed that the gene expression levels of CLE9, FA, PUCHI, UF, CLV3, LOB30, SFT, S-WOX9 and SVP were significantly different in the two materials. Endogenous hormone analysis and exogenous hormone treatment revealed a variety of plant hormones involved in flowering reversion in tomato. Thus, tomato flowering reversion was studied comprehensively by transcriptome analysis for the first time, providing new insights for the study of flower development regulation in tomato and other plants.

Study of genetic modifications of flower development and methylation status in phytoplasma infected Brassica (Brassica rapa L.).

The plants of B. rapa (syn. B. campestris) are the most important food crop of Pakistan for the production of cooking oil. Brassica plants infected by phytoplasma exhibit floral abnormalities including phyllody, virescence, hypertrophied sepal and aborted reproductive organs and affected flower developmental genes which reduces the yield manifold. The expression level of flower developmental genes in healthy and phytoplasma infected brassica were compared by using semi-quantitative reverse transcription polymerase chain reaction and DNA hybridization. In infected brassica, LEAFY (LFY) gene, controlling the development and maintenance of floral organ, and directly involved in controlling the homeotic gene expression was affected, while APETALA2, regulate the production of sepals and petals, were not altered. Whereas the genes WUSCHEL, APETALA3 and AGAMOUS, were significantly down-regulated, that were responsible for the identity of shoot and central meristem, petals and stamens production, and stamens and carpels development, respectively. The GLUB gene, controlling the production of β-1,3-glucanases enzyme, was highly up-regulated. According to DNA hybridization results, AGAMOUS and APETALA3 were restricted to floral organs territories in healthy and phytoplasma infected brassica, indicating that their expression was tissue-specific. These outcomes indicated that flower abnormalities of phytoplasma infected B. rapa are linked with DNA methylation in the expression of homeotic genes regulating flower development. Azacitidine act as a DNA demethylating reagent. By applying the foliar spray of azacitidine during the flower development, cells of Phytoplasma infected plants exhibits demethylation of DNA when treated with azacitidine chemical that incorporated as analogue of cytosine during the cell division stage. B. rapa showed the up-regulation of gene expression level significantly that restore the normal production of flowers, ultimately increase the oil production throughout the world.

Characterization of YABBY genes in Dendrobium officinale reveals their potential roles in flower development.

TheseYABBY genes are transcription factors (TFs) that play crucial roles in various developmental processes in plants. There is no comprehensive characterization of YABBY genes in a valuable Chinese orchid herb, Dendrobium officinale. In this study, a total of nine YABBY genes were identified in the D. officinale genome. These YABBY genes were divided into four subfamilies: CRC/DL, FIL, INO, and YAB2. Expression pattern analyses showed that eight of the YABBY genes were strongly expressed in reproductive organs (flower buds) but weakly expressed in vegetative organs (roots, leaves, and stems). DoYAB1, DoYAB5, DoDL1, and DoDL3 were abundant in the small flower bud stage, while DoDL2 showed no changes throughout flower development. In addition, DoDL1-3 genes were strongly expressed in the column, tenfold more than in sepals, petals, and the lip. DoYAB1 from the FIL subfamily, DoYAB2 from the YAB2 subfamily, DoYAB3 from the INO subfamily, and DoDL2 and DoDL3 from the CRC/DL subfamily were selected for further analyses. Subcellular localization analysis showed that DoYAB1-3, DoDL2, and DoDL3 were localized in the nucleus. DoYAB2 and DoYAB3 interacted strongly with DoWOX2 and DoWOX4, while DoYAB1 showed a weak interaction with DoWOX4. These results reveal a regulatory network involving YABBY and WOX proteins in D. officinale. Our data provide clues to understanding the role of YABBY genes in the regulation of flower development in this orchid and shed additional light on the function of YABBY genes in plants.

Transcriptome Analysis Reveals the Role of GA3 in Regulating the Asynchronism of Floral Bud Differentiation and Development in Heterodichogamous Cyclocarya paliurus (Batal.) Iljinskaja.

Cyclocarya paliurus is an important medical plant owing to the diverse bioactive compounds in its leaves. However, the heterodichogamy with female and male functions segregation within protandry (PA) or protogyny (PG) may greatly affect seed quality and its plantations for medicinal use. To speculate on the factor playing the dominant role in regulating heterodichogamy in C. paliurus, based on phenotypic observations, our study performed a multi comparison transcriptome analysis on female and male buds (PG and PA types) using RNA-seq. For the female and male bud comparisons, a total of 6753 differentially expressed genes (DEGs) were detected. In addition, functional analysis revealed that these DEGs were significantly enriched in floral development, hormone, and GA-related pathways. As the dominant hormones responsible for floral differentiation and development, gibberellins (GAs) in floral buds from PG and PA types were quantified using HPLC-MS. Among the tested GAs, GA3 positively regulated the physiological differentiation (S0) and germination (S2) of floral buds. The dynamic changes of GA3 content and floral morphological features were consistent with the expression levels of GA-related genes. Divergences of GA3 contents at S0 triggered the asynchronism of physiological differentiation between male and female buds of intramorphs (PA-M vs. PA-F and PG-F vs. PG-M). A significant difference in GA3 content enlarged this asynchronism at S2. Thus, we speculate that GA3 plays the dominant role in the formation of heterodichogamy in C. paliurus. Meanwhile, the expression patterns of GA-related DEGs, including CPS, KO, GA20ox, GA2OX, GID1, and DELLA genes, which play central roles in regulating flower development, coincided with heterodichogamous characteristics. These results support our speculations well, which should be further confirmed.

MicroRNA172 controls inflorescence meristem size through regulation of APETALA2 in Arabidopsis.

The APETALA2 (AP2) transcription factor regulates flower development, floral transition and shoot apical meristem (SAM) maintenance in Arabidopsis. AP2 is also regulated at the post-transcriptional level by microRNA172 (miR172), but the contribution of this to SAM maintenance is poorly understood. We generated transgenic plants carrying a form of AP2 that is resistant to miR172 (rAP2) or carrying a wild-type AP2 susceptible to miR172. Phenotypic and genetic analyses were performed on these lines and mir172 mutants to study the role of AP2 regulation by miR172 on meristem size and the rate of flower production. We found that rAP2 enlarges the inflorescence meristem by increasing cell size and cell number. Misexpression of rAP2 from heterologous promoters showed that AP2 acts in the central zone (CZ) and organizing center (OC) to increase SAM size. Furthermore, we found that AP2 is negatively regulated by AUXIN RESPONSE FACTOR 3 (ARF3). However, genetic analyses indicated that ARF3 also influences SAM size and flower production rate independently of AP2. The study identifies miR172/AP2 as a regulatory module controlling inflorescence meristem size and suggests that transcriptional regulation of AP2 by ARF3 fine-tunes SAM size determination.

Comprehensive Analyses of Four PtoNF-YC Genes from Populus tomentosa and Impacts on Flowering Timing.

Flowering is an important link in the life process of angiosperms, and it is also an important sign of the transformation of plants from vegetative to reproductive growth. Although the flowering regulation network of Arabidopsis is well-understood, there has been little research on the molecular mechanisms of perennial woody plant flower development regulation. Populus tomentosa is a unique Chinese poplar species with fast growth, strong ecological adaptability, and a long lifecycle. However, it has a long juvenile phase, which seriously affects its breeding process. Nuclear factor-Y (NF-Y) is an important type of transcription factor involved in the regulation of plant flowering. However, there are few reports on PtoNF-Y gene flowering regulation, and the members of the PtNF-YC subfamily are unknown. In this study, four key genes were cloned and analyzed for sequence characteristics, gene structure, genetic evolution, expression patterns, and subcellular localization. The plant expression vector was further constructed, and transgenic Arabidopsis and P. tomentosa plants were obtained through genetic transformation and a series of molecular tests. The flowering time and other growth characteristics were analyzed. Finally, the expression level of flowering genes was detected by quantitative PCR, the interaction between PtoNF-YC and PtoCOL proteins was measured using the yeast two-hybrid system to further explain the flowering regulation mechanism, and the molecular mechanisms by which PtNF-YC6 and PtNF-YC8 regulate poplar flowering were discussed. These results lay the foundation for elucidating the molecular regulation mechanism of PtoNF-YC in flowering and furthering the molecular design and breeding of poplar, while providing a reference for other flowering woody plants.

Comparative proteome analysis reveals the role of negative floral regulators and defense-related genes in phytoplasma infected sesame.

"Candidatus Phytoplasma australiense" is associated with floral malformations in sesame but the interaction remains largely unexplored. A label-free quantitative shotgun proteomics approach through liquid chromatography-mass spectrometry quadruple time-of-flight was used to analyze changes in the proteome of asymptomatic (control) and symptomatic (phytoplasma-infected) sesame plants to identify proteins differentially expressed during phytoplasma infection at early stages of flower development. A total of 3457 and 1704 proteins were identified from asymptomatic and symptomatic samples respectively through proteome profiling with three runs per sample. Several differentially abundant proteins (DAPs) were identified which might be involved in sesame-phytoplasma interaction. The DAPs identified were related to transcription, cell division, chromosome partitioning, defense mechanisms, negative regulation of flower development, amino acid transport and metabolism, signal transduction and RNA processing, and its modifications. Of these proteins, 21 were downregulated while 212 were significantly upregulated in symptomatic sesame plants compared to the control plants. The floral development-related proteins like UBP16 and DCAF1 were found to be downregulated while negative regulators/repressors of floral development genes, HUA2, PIE1, and ICU2, were upregulated in symptomatic samples indicating phytoplasma's role in altering the expression of these genes. Validation of these genes through quantitative retro-transcripted PCR suggested that the DAPs observed in symptomatic sesame might be induced by phytoplasma presence to suppress flowering via negative regulation of flower development.

Exogenous GA3 promotes flowering in Paphiopedilum callosum (Orchidaceae) through bolting and lateral flower development regulation.

Paphiopedilum orchids have a high ornamental value, and their flower abundance and timing are both key horticultural traits regulated by phytohormones. All one-flowered Paphiopedilum have additional lateral buds in the apical bract that fail to develop. In this study, an exogenous gibberellin (GA3) application promoted flowering of Pathiopedilum callosum by inducing its early bolting instead of the floral transition of dominant flowers. Applying GA3 effectively promoted lateral flower differentiation, resulting in a two-flowered inflorescence. GA-promoted lateral flower formation involved GA interacting with indole-3-acetic acid (IAA) and cytokinins (CTKs), given the decreased CTK content and downregulated expression of CTK synthesis genes, the increased IAA content and downregulated expression of IAA degradation, and the upregulated expression of transport genes. Further, GA acted via PcDELLA, PcTCP15, and PcXTH9 expressed in stage 5 to promote bolting, and via expression of PcAP3, PcPI, and PcSEP to promote flowering. This study provides insight into mechanisms regulating flower development of P. callosum.

The Cymbidium genome reveals the evolution of unique morphological traits

The marvelously diverse Orchidaceae constitutes the largest family of angiosperms. The genus Cymbidium in Orchidaceae is well known for its unique vegetation, floral morphology, and flower scent traits. Here, a chromosome-scale assembly of the genome of Cymbidium ensifolium (Jianlan) is presented. Comparative genomic analysis showed that C. ensifolium has experienced two whole-genome duplication (WGD) events, the most recent of which was shared by all orchids, while the older event was the τ event shared by most monocots. The results of MADS-box genes analysis provided support for establishing a unique gene model of orchid flower development regulation, and flower shape mutations in C. ensifolium were shown to be associated with the abnormal expression of MADS-box genes. The most abundant floral scent components identified included methyl jasmonate, acacia alcohol and linalool, and the genes involved in the floral scent component network of C. ensifolium were determined. Furthermore, the decreased expression of photosynthesis-antennae and photosynthesis metabolic pathway genes in leaves was shown to result in colorful striped leaves, while the increased expression of MADS-box genes in leaves led to perianth-like leaves. Our results provide fundamental insights into orchid evolution and diversification.

Biochemical Changes and Antioxidant Variations in Date Palm (Phoenix dactylifera L.) Varieties during Flower Induction and Development.

The present investigation was carried out to explore the biochemical changes and antioxidant variations, including non-enzymatic and enzymatic antioxidant variations, in the leaves of different varieties of date palm (Phoenix dactylifera L.) belonging to the early, mid-, and late-flowering categories in the United Arab Emirates. The changes in the protein and phenol concentration; the ascorbic acid, reduced glutathione, and α-tocopherol contents; and the activity of peroxidase and polyphenol oxidase were studied in the leaves during the preflowering, flowering, and postflowering stages of the date palms. Two varieties each from the early (Shaham, Khanezi), mid- (Barhee, Nabthasaif), and late- (Khasab, Fardh) flowering types were used in this study. The protein content in the leaves was higher in the early flowering varieties during the preflowering stage but lower in the other two varieties. The phenol content showed an opposite trend to the protein. There was significant variation in the ascorbic acid content and a reduction in glutathione and α-tocopherol between the leaves of different varieties. Similarly, the activity of the antioxidant enzyme ascorbate peroxidase in the leaves was higher during the preflowering stage in all varieties. The superoxide dismutase (SOD), polyphenol oxidase (PPO), and catalase (CAT) activity was highest in the Bharhee leaves for all the stages. The peroxidase activity (POD) was highest in the Fardh variety of date palm, whereas the Khanezi variety exhibited the lowest activity. This study can be used as a baseline for developing more protocols for understanding the possible roles of biochemicals, antioxidants, antioxidant enzymes, and their interactions in the regulation of flower development in different date palm varieties.

Cloning, Expression, and Tobacco Overexpression Analyses of a PISTILLATA/GLOBOSA-like (OfGLO1) Gene from Osmanthus fragrans.

GLOBOSA (GLO), a B-class MADS-box gene, is involved in floral organ determination but has rarely been studied in Osmanthus fragrans, which is a very popular ornamental tree species in China. Here, the full-length cDNA of a homologous GLO1 gene (named OfGLO1) was cloned from a flower bud of O. fragrans using the RACE technique. The OfGLO1 has a 645 bp open reading frame, encoding 214 amino acids. Similar to other PI/GLO proteins, OfGLO1 has two conserved domains, MADS MEF2-like and K-box, and a 16-amino-acid PI motif in the C terminal region. Our phylogeny analysis classified OfGLO1 as a PI-type member of the B-class MADS-box gene family. The qRT-PCR assay showed that the expression of OfGLO1 in O. fragrans was continuously upregulated from the tight bud stage to the full flowering stage but barely expressed in the pistils, sepals, and non-floral organs, such as root, leaf, and stem. The genetic effect of OfGLO1 was assayed by ectopic expression in tobacco plants. Compared with the wild-type, OfGLO1 transformants showed reduced plant size, earlier flowering, shorter stamens, and lower seed setting rates. Furthermore, some stamens were changed into petal-like structures. These findings indicate that OfGLO1 plays an important role in the regulation of flower development. This study improved our understanding of class B gene function in woody plants.

Discovering candidate genes related to flowering time in the spring panel of Camelina sativa

Camelina sativa is a promising oilseed and industrial crop that benefits sustainable food, feed and fuel industries. Early flowering is critical for local adaptation as well as maximizing yield in Camelina sativa. Even though the preliminary data indicated wide variation in flowering time in the spring camelina germplasm, our understanding of underlying genes and their roles in regulating flower development is still limited. The current study combined genotypic data and flowering time from the spring panel, followed by genome-wide association study (GWAS) and whole-genome prediction to identify significant trait-associated markers and evaluate the predictive capability of the entire marker set. The analysis of phenotypic data showed significant genotypic and environmental effects on flowering time. A high heritability of 0.893 in flowering time suggests effectiveness of breeding early flowering camelina varieties. The GWAS analysis identified 20 significant trait-associated single nucleotide polymorphisms (SNPs) that colocalized within/or near a variety of transcription factors (e.g. SUPPRESSOR of PHYA-1/SPA1, BES1-INTERACTING MYC-LIKE 1/BIM1) or protein families containing specific functional domains (e.g. CCCH zinc finger protein family and B3-DNA binding domain containing protein family). These transcription factors were known to interact with key regulatory genes in the four major pathways (i.e. photoperiod, autonomous, vernalization and gibberellic acid pathways) to cooperatively regulate floral transition in arabidopsis. Whole-genome prediction showed a low-to-moderate predictive ability (0.559) to improve early flowering trait in camelina. This study is the first step for future in-depth exploration and genetic improvements of flower development and timing in camelina for breeding.

Gibberellin Induced Transcriptome Profiles Reveal Gene Regulation of Loquat Flowering

Flowering is an integral part of the life cycle of flowering plants, which is essential for plant survival and crop production. Most woody fruit trees such as apples and pears bloom in spring, but loquat blooms in autumn and winter. Gibberellin (GA) plays a key role in the regulation of plant flower formation. In this study, we sprayed loquat plants with exogenous GA3, which resulted in vigorous vegetative growth rather than floral bud formation. We then performed a comprehensive RNA-seq analysis on GA3-treated and control-treated leaves and buds over three time periods to observe the effects of exogenous GA3 application on floral initiation and development. The results showed that 111 differentially expressed genes (DEGs) and 563 DEGs were down-regulated, and 151 DEGs and 506 DEGs were up-regulated in buds and leaves, respectively, upon treatment with GA3. Among those that are homologs of the DELLA-mediated GA signal pathway genes, some may be involved in the positive regulation of flower development, including EjWRKY75, EjFT, EjSOC1, EjAGL24, EjSPL, EjLFY, EjFUL, and EjAP1; while some may be involved in the negative regulation of flower development, including EjDELLA, EjMYC3, EjWRKY12, and EjWRKY13. Finally, by analyzing the co-expression of DEGs and key floral genes EjSOC1s, EjLFYs, EjFULs, EjAP1s, 330 candidate genes that may be involved in the regulation of loquat flowering were screened. These genes belong to 74 gene families, including Cyclin_C, Histone, Kinesin, Lipase_GDSL, MYB, P450, Pkinase, Tubulin, and ZF-HD_dimer gene families. These findings provide new insights into the regulation mechanism of loquat flowering.

Genome-wide identification and evolutionary analysis of MLO gene family in Rosaceae plants

Mutants lacking wild-type MLO (Mildew resistance Locus O) proteins show broad-spectrum resistance to the powdery mildew fungus, and dysregulated cell death control, with spontaneous cell death in response to developmental or abiotic stimuli. In order to understand the evolution and divergence patterns of the MLO gene family in Rosaceae plants, we analysed systematically genome-wide data from Fragaria vesca, Prunus persica, Prunus mume, Malus domestica, Pyrus bretschneideri and Rubus occidentalis based on bioinformatics methods. Using three phylogenetic methods (the neighbour-joining, maximum likelihood, and Bayesian methods), we identified 117 MLO genes from 6 Rosaceae species. The results of all three phylogenetic analysis methods supported that these genes were divided into six clades. Conserved motif analysis found that only motif 2 was present in all MLO proteins and had 3 nearly invariant amino acid residues. The findings indicated that motif 2 might be shared by the MLO gene family. The structural features of these genes showed large variations in sequence length among different species, although the lengths and the numbers of exons exhibited high degrees of similarity. Selective pressure analysis showed extremely significant differences in all 6 clades, with 2, 1, and 1 site(s) under significant positive selection detected in clades III, IV, and VI, respectively. These positive selection sites were important driving forces for the promotion of the functional differentiation of the MLO genes. Functional divergence analysis showed that the significantly divergent sites were located within the domains of the MLO genes. Functional distance analysis showed that the clade V had more conservative functions and might have retained more original functions during the evolutionary process. However, clade I may have undergone extensive altered functional constraints as a specialised functional role. Moreover, the most original function of the MLO genes in Rosaceae could be related to the evolution of their resistance to powdery mildew, which then gradually evolved into functions such as the regulation of flower development, the control of root morphology, and seed evolution due to the different evolutionary rates after gene duplication. These results provide a theoretical basis for further studies of the molecular evolutionary patterns of the plant MLO gene family.

Mapping and candidate gene analysis of silique number mutant in <italic>Brassica napus </italic>L.

<p id="C3">The silique number is one of the important components of yield per plant in oilseed rape (<italic>Brassica napus </italic>L.) and the exploitation and utilization of its excellent alleles are essential to increase yield. More than hundreds of silique number QTLs have been mapped in oilseed rape, but they are difficult to be fine-mapped or cloned because of their moderate and unstable effects. A oilseed rape mutant (No.7931) was detected in previous study and it had few siliques at mature stage due to the stop growth after differentiation about 10 flowers on the top of inflorescence. A F₂ segregating population consisting of 3400 individuals was constructed using this mutant and another more-silique lines No.73290. Among them, we performed BSA-seq on 30 individuals with extreme more- or less-siliques and detected three associated intervals of 0-1.1 Mb, 4.7-6.2 Mb, and 11.5-12.4 Mb on the C02 chromosome. These genomic intervals contained a total of 522 annotated genes in the reference genome DarmorV8.1, among which 235 genes had functional annotation and SNP/InDel variation. At the early stage of flower bud differentiation, the shoot apical meristems of two parents were subjected to RNA-seq, and a total of 8958 differentially expressed genes (DEGs) were detected. These DEGs were significantly enriched into 20 pathways, including carbohydrate metabolism, translation, and amino acid metabolism (highly associated with flower bud differentiation) and so on, among which 99 were located in the associated intervals. By the integration of gene functional annotation as well as sequence and expression variation analysis, a total of nine candidate genes (<italic>BnaC02g00490.1D2</italic>,<italic> BnaC02g01030.1D2</italic>,<italic> BnaC02g01120.1D2</italic>,<italic> BnaC02g00270.1D2</italic>,<italic> BnaC02g02670.1D2</italic>,<italic> BnaC02g08680.1D2</italic>,<italic> BnaC02g08890.1D2</italic>,<italic> BnaC02g09480.1D2</italic>, and <italic>BnaC02g10490.1D2</italic>) were identified, which were mainly involved in the maintenance of inflorescence meristems and the regulation of flower development. The above results lay the foundation for the following fine-mapping and cloning of the silique number mutant gene in oilseed rape.