Overexpression of the CmJAZ1-like gene delays flowering in Chrysanthemum morifolium

Multi-locus genome-wide association studies reveal the dynamic genetic architecture of flowering time in chrysanthemum

KEY MESSAGE

The dynamic genetic architecture of flowering time in chrysanthemum was elucidated by GWAS. Thirty-six known genes and 14 candidate genes were identified around the stable QTNs and QEIs, among which ERF-1 was highlighted. Flowering time (FT) adaptation is one of the major breeding goals in chrysanthemum, a multipurpose ornamental plant. In order to reveal the dynamic genetic architecture of FT in chrysanthemum, phenotype investigation of ten FT-related traits was conducted on 169 entries in 2 environments. The broad-sense heritability of five non-conditional FT traits, i.e., budding (FBD), visible coloring (VC), early opening (EO), full-bloom (OF) and decay period (DP), ranged from 56.93 to 84.26%, which were higher than that of the five derived conditional FT traits (38.51-75.13%). The phenotypic variation coefficients of OF_EO and DP_OF were relatively large ranging from 30.59 to 36.17%. Based on 375,865 SNPs, the compressed variance component mixed linear model 3VmrMLM was applied for a multi-locus genome-wide association study (GWAS). As a result, 313 quantitative trait nucleotides (QTNs) were identified for the non-conditional FT traits in single-environment analysis, while 119 QTNs and 67 QTN-by-environment interactions (QEIs) were identified in multi-environment analysis. As for the conditional traits, 343 QTNs were detected in single-environment analysis, and 119 QTNs and 83 QEIs were identified in multi- environment analysis. Among the genes around stable QTNs and QEIs, 36 were orthologs of known FT genes in Arabidopsis and other plants; 14 candidates were mined by combining the transcriptomics data and functional annotation, including ERF-1, ACA10, and FOP1. Furthermore, the haplotype analysis of ERF-1 revealed six elite accessions with extreme FBD. Our findings contribute to the understanding of dynamic genetic architecture of FT and provide valuable resources for future chrysanthemum molecular breeding programs.

Multi-locus genome-wide association study and genomic prediction for flowering time in chrysanthemum

MAIN CONCLUSION

Multi-locus GWAS detected several known and candidate genes responsible for flowering time in chrysanthemum. The associations could greatly increase the predictive ability of genome selection that accelerates the possible application of GS in chrysanthemum breeding. Timely flowering is critical for successful reproduction and determines the economic value for ornamental plants. To investigate the genetic architecture of flowering time in chrysanthemum, a multi-locus genome-wide association study (GWAS) was performed using a collection of 200 accessions and 330,710 single-nucleotide polymorphisms (SNPs) via 3VmrMLM method. Five flowering time traits including budding (FBD), visible colouring (VC), early opening (EO), full-bloom (OF) and senescing (SF) stages, plus five derived conditional traits were recorded in two environments. Extensive phenotypic variations were observed for these flowering time traits with coefficients of variation ranging from 6.42 to 38.27%, and their broad-sense heritability ranged from 71.47 to 96.78%. GWAS revealed 88 stable quantitative trait nucleotides (QTNs) and 93 QTN-by-environment interactions (QEIs) associated with flowering time traits, accounting for 0.50-8.01% and 0.30-10.42% of the phenotypic variation, respectively. Amongst the genes around these stable QTNs and QEIs, 21 and 10 were homologous to known flowering genes in Arabidopsis; 20 and 11 candidate genes were mined by combining the functional annotation and transcriptomics data, respectively, such as MYB55, FRIGIDA-like, WRKY75 and ANT. Furthermore, genomic selection (GS) was assessed using three models and seven unique marker datasets. We found the prediction accuracy (PA) using significant SNPs identified by GWAS under SVM model exhibited the best performance with PA ranging from 0.90 to 0.95. Our findings provide new insights into the dynamic genetic architecture of flowering time and the identified significant SNPs and candidate genes will accelerate the future molecular improvement of chrysanthemum.

The RAV transcription factor TEMPRANILLO1 involved in ethylene-mediated delay of chrysanthemum flowering

TEMPRANILLO1 (TEM1) is a transcription factor belonging to related to ABI3 and VP1 family, which is also known as ethylene response DNA-binding factor 1 and functions as a repressor of flowering in Arabidopsis. Here, a putative homolog of AtTEM1 was isolated and characterized from chrysanthemum, designated as CmTEM1. Exogenous application of ethephon leads to an upregulation in the expression of CmTEM1. Knockdown of CmTEM1 promotes floral initiation, while overexpression of CmTEM1 retards floral transition. Further phenotypic observations suggested that CmTEM1 involves in the ethylene-mediated inhibition of flowering. Transcriptomic analysis established that expression of the flowering integrator CmAFL1, a member of the APETALA1/FRUITFULL subfamily, was downregulated significantly in CmTEM1-overexpressing transgenic plants compared with wild-type plants but was verified to be upregulated in amiR-CmTEM1 lines by quantitative RT-PCR. In addition, CmTEM1 is capable of binding to the promoter of the CmAFL1 gene to inhibit its transcription. Moreover, the genetic evidence supported the notion that CmTEM1 partially inhibits floral transition by targeting CmAFL1. In conclusion, these findings demonstrate that CmTEM1 acts as a regulator of ethylene-mediated delayed flowering in chrysanthemum, partly through its interaction with CmAFL1.

FUL homologous gene CmFL1 is involved in regulating flowering time and floret numbers in Chrysanthemum morifolium

Flowering time and floret numbers are important ornamental characteristics of chrysanthemums that control their adaptability and inflorescence morphology, respectively. The FRUITFULL (FUL) gene plays a key role in inducing flowering and inflorescence meristem development. In this study, we isolated a homolog of the MADS-box gene FUL, CmFUL-Like 1 (CmFL1), from chrysanthemum inflorescence buds. Quantitative RT-PCR and in situ analyses showed that CmFL1 was strongly expressed in young inflorescence buds. Overexpression of CmFL1 caused early flowering while co-suppression expression of CmFL1 increased the number of florets. Furthermore, the floral promoting factors CmSOC1, CmFDL1, and CmLFY were up-regulated in the shoot tips of transgenic plants. In addition, RNA-seq analysis of the transgenic plants suggested that certain differentially expressed genes (DEGs)-such as MADS-box, homeobox family, and ethylene pathway genes-may be involved in the inflorescence meristem development. GO pathway enrichment analysis showed that the differentially transcribed genes enriched the representation of the carbohydrate metabolic pathway, which is critical for flower development. Overall, our findings revealed the conserved function of CmFL1 in controlling flowering time along with a novel function in regulating the number of florets.

MADS-box protein PpDAM6 regulates chilling requirement-mediated dormancy and bud break in peach

Bud dormancy is crucial for winter survival and is characterized by the inability of the bud meristem to respond to growth-promotive signals before the chilling requirement (CR) is met. However, our understanding of the genetic mechanism regulating CR and bud dormancy remains limited. This study identified PpDAM6 (DORMANCY-ASSOCIATED MADS-box) as a key gene for CR using a genome-wide association study analysis based on structural variations in 345 peach (Prunus persica (L.) Batsch) accessions. The function of PpDAM6 in CR regulation was demonstrated by transiently silencing the gene in peach buds and stably overexpressing the gene in transgenic apple (Malus × domestica) plants. The results showed an evolutionarily conserved function of PpDAM6 in regulating bud dormancy release, followed by vegetative growth and flowering, in peach and apple. The 30-bp deletion in the PpDAM6 promoter was substantially associated with reducing PpDAM6 expression in low-CR accessions. A PCR marker based on the 30-bp indel was developed to distinguish peach plants with non-low and low CR. Modification of the H3K27me3 marker at the PpDAM6 locus showed no apparent change across the dormancy process in low- and non-low- CR cultivars. Additionally, H3K27me3 modification occurred earlier in low-CR cultivars on a genome-wide scale. PpDAM6 could mediate cell-cell communication by inducing the expression of the downstream genes PpNCED1 (9-cis-epoxycarotenoid dioxygenase 1), encoding a key enzyme for ABA biosynthesis, and CALS (CALLOSE SYNTHASE), encoding callose synthase. We shed light on a gene regulatory network formed by PpDAM6-containing complexes that mediate CR underlying dormancy and bud break in peach. A better understanding of the genetic basis for natural variations of CR can help breeders develop cultivars with different CR for growing in different geographical regions.

The Cm14-3-3μ protein and CCT transcription factor CmNRRa delay flowering in chrysanthemum

Floral transition from vegetative to reproductive growth is pivotal in the plant life cycle. NUTRITION RESPONSE AND ROOT GROWTH (OsNRRa) as a CONSTANS, CONSTANS-LIKE, TOC1 (CCT) domain protein delays flowering in rice and an orthologous gene CmNRRa inhibits flowering in chrysanthemum; however, the mechanism remains unknown. In this study, using yeast two-hybrid screening, we identified the 14-3-3 family member Cm14-3-3µ as a CmNRRa-interacting protein. Biochemical assays using a combination of bimolecular fluorescence complementation (BiFC), pull-down, and Co-immunoprecipitation (Co-IP) were performed to confirm the physical interaction between CmNRRa and Cm14-3-3µ in chrysanthemum. In addition, expression analysis showed that CmNRRa, but not Cm14-3-3µ, responded to the diurnal rhythm, whereas both genes were highly expressed in the leaves. Moreover, the function in flowering time regulation of Cm14-3-3µ is similar to that of CmNRRa. Furthermore, CmNRRa repressed chrysanthemum FLOWERING LOCUS T-like 3 (CmFTL3) and APETALA 1 (AP1)/FRUITFULL (FUL)-like gene (CmAFL1), but induced TERMINAL FLOWER1 (CmTFL1) directly by binding to their promoters. Cm14-3-3µ enhanced the ability of CmNRRa to regulate the expression of these genes. These findings suggest that there is a synergistic relationship between CmNRRa and Cm14-3-3µ in flowering repression in chrysanthemum.

CmERF5-CmRAP2.3 transcriptional cascade positively regulates waterlogging tolerance in Chrysanthemum morifolium

Waterlogging stress affects plant growth by limiting root respiration and reducing yield and economic value. Therefore, identifying genes involved in regulating waterlogging stress is vital. This study reports the ethylene-responsive VII transcription factor (CmRAP2.3) in the chrysanthemum. Subcellular localization and transactivation assay analyses revealed that CmRAP2.3 was localized in the nucleus and possessed transactivation activity. Overexpression of CmRAP2.3 in chrysanthemum was found to enhance waterlogging tolerance by decreasing reactive oxygen species (ROS) levels. Furthermore, we found that the transcription factor CmERF5 binds to GCC-like motifs in the CmRAP2.3 promoter region and activates CmRAP2.3 expression. Additionally, CmERF5 overexpression maintained a low ROS level and improved chrysanthemum waterlogging tolerance. Taken together, this study shows a molecular mechanism by which CmERF5 transcriptionally activates CmRAP2.3 to reduce waterlogging stress via the ROS pathway in the chrysanthemum.

An ethylene-responsive transcription factor and a B-box protein coordinate vegetative growth and photoperiodic flowering in chrysanthemum

Plants employ several endogenous and exogenous signals to guarantee timely floral transitions with floral integrators. To avoid premature flowering, flowering plants must control the balance between vegetative and floral development. As a Group II member of BBX family, CmBBX8 promotes flowering by directly activating CmFTL1 in summer-flowering chrysanthemum. However, the mechanisms underlying this floral transition is yet to be elucidated. Here, we report that the chrysanthemum ERF3 homologue, CmERF3, physically interacts with CmBBX8 through yeast two-hybrid (Y2H), bimolecular fluorescence complementation (BiFC), pull-down, and luciferase complementation (LCI) assays. We found that CmERF3 was highly expressed at the vegetative stage and rarely expressed in the reproductive phase, indicating that CmERF3 may play a critical role in maintaining vegetative growth to prevent premature flowering. Rhythm analysis revealed that CmERF3 had a different response to rhythm compared to CmBBX8. Knockdown of CmERF3 facilitated floral initiation, whereas overexpression of CmERF3 delayed floral transition. We further found that CmERF3 repressed the transactivation activity of CmBBX8 on the downstream CmFTL1 gene. Collectively, our results indicate that the CmERF3-CmBBX8 transcriptional complex is a crucial module that balances the vegetative growth and reproductive development of chrysanthemum.

The TIFY family protein CmJAZ1-like negatively regulates petal size via interaction with the bHLH transcription factor CmBPE2 in Chrysanthemum morifolium

Petals are the second floral whorl of angiosperms, exhibiting astonishing diversity in their size between and within species. This variation is essential for protecting their inner reproductive organs and attracting pollinators for fertilization. However, currently, the genetic and developmental control of petal size remains unexplored. Chrysanthemum (Chrysanthemum morifolium) belongs to the Asteraceae family, the largest group of angiosperms, and the extraordinary diversity of petal size in chrysanthemums makes it an ideal model for exploring the regulation mechanism of petal size. Here, we reveal that overexpression of a JAZ repressor CmJAZ1-like exhibits decreased petal size compared to that of the wild-type as a result of repressed cell expansion. Through further in-depth exploration, we confirm an interaction pair between CmJAZ1-like and the bHLH transcription factor CmBPE2. The inhibition of CmBPE2 expression negatively regulates petal size by downregulating the expression of genes involved in cell expansion. Furthermore, CmJAZ1-like significantly reduced the activation ability of CmBPE2 on its target gene CmEXPA7 by directly interacting with it, thus participating in the regulation of petal size development in chrysanthemum. Our results will provide insights into the molecular mechanisms of petal size regulation in flowering plants.

The transcriptional coactivator CmMBF1c is required for waterlogging tolerance in Chrysanthemum morifolium

Waterlogging is one of the most serious abiotic stressors affecting Chrysanthemum morifolium during its lifespan. However, the molecular mechanisms underlying the waterlogging tolerance of chrysanthemum remain unclear. In this study, we discovered that the transcriptional coactivator MULTIPROTEIN BRIDGING FACTOR 1c (CmMBF1c) was significantly induced by waterlogging stress in chrysanthemums. Promoter sequence analysis and transient dual-luciferase assay using chrysanthemum protoplasts showed that the waterlogging-tolerant cultivar 'Nannongxuefeng' carried more response elements involved in waterlogging and hypoxia stress compared with the waterlogging-sensitive cultivar 'Qinglu', conferring on 'Nannongxuefeng' a stronger hypoxia responsive activity and higher CmMBF1c expression under waterlogging conditions. Subcellular localization and transcriptional activity assays showed that CmMBF1c protein was localized to the nucleus and had no transcriptional activation activity. Overexpression of CmMBF1c in 'Qinglu' enhanced its waterlogging tolerance by promoting its reactive oxygen species (ROS) scavenging ability and maintaining low ROS levels. However, RNAi-mediated knockdown of CmMBF1c in cultivar 'Nannongxuefeng' resulted in the opposite tendency. Yeast two-hybrid screening and tobacco bimolecular fluorescence complementation assays revealed that CmHRE2, a pivotal regulator of hypoxia response, could interact with CmMBF1c. In summary, this study demonstrates that CmMBF1c improves chrysanthemum waterlogging tolerance by regulating its ROS signaling pathway and interacting with CmHRE2. These findings together offer, to our knowledge, new mechanistic insights into chrysanthemum waterlogging tolerance and provide a rational foundation for future research on the genetic improvement of horticultural crops for waterlogging stress tolerance.

An ethylene-responsive transcription factor and a flowering locus KH domain homologue jointly modulate photoperiodic flowering in chrysanthemum

The timely transition from vegetative to reproductive development is coordinated through the quantitative regulation of floral pathway genes in response to physiological and environmental cues. The function of ethylene-responsive element-binding protein (ERF) transcription factors in the regulation of flowering in chrysanthemum (Chrysanthemum morifolium Ramat.) is not well understood. Here, chrysanthemum overexpressing CmERF110 flowered earlier than the wild-type plants, while those in which CmERF110 was suppressed flowered later. RNA-seq results revealed that several genes involved in the circadian rhythm were transcribed differently in CmERF110 transgenic plants from that of the wild-type plants. The rhythm peak of the circadian clock genes in transgenic plants was delayed. Yeast two-hybrid screening of CmERF110 interactors identified a chrysanthemum FLOWERING LOCUS KH DOMAIN (FLK) homologue CmFLK, which was further confirmed with both in vitro and in vivo assays. KEGG pathway enrichment also revealed that CmFLK is involved in the regulation of circadian rhythm-related genes. CmFLK transgenic plants showed a change in flowering time and delayed rhythm peak of the circadian rhythm genes. Taken together, the present data not only suggest that CmERF110 interacts with CmFLK to promote floral transition by tuning the circadian clock, but also provides evidence for the evolutionary conservation of the components in the autonomous pathway in chrysanthemum.

A regulatory GhBPE-GhPRGL module maintains ray petal length in Gerbera hybrida

The molecular mechanism regulating petal length in flowers is not well understood. Here we used transient transformation assays to confirm that GhPRGL (proline-rich and GASA-like)-a GASA (gibberellic acid [GA] stimulated in Arabidopsis) family gene-promotes the elongation of ray petals in gerbera (Gerbera hybrida). Yeast one-hybrid screening assay identified a bHLH transcription factor of the jasmonic acid (JA) signaling pathway, here named GhBPE (BIGPETAL), which binds to the GhPRGL promoter and represses its expression, resulting in a phenotype of shortened ray petal length when GhBPE is overexpressed. Further, the joint response to JA and GA of GhBPE and GhPRGL, together with their complementary expression profiles in the early stage of petal growth, suggests a novel GhBPE-GhPRGL module that controls the size of ray petals. GhPRGL promotes ray petal elongation in its early stage especially, while GhBPE inhibits ray petal elongation particularly in the late stage by inhibiting the expression of GhPRGL. JA and GA operate in concert to regulate the expression of GhBPE and GhPRGL genes, providing a regulatory mechanism by which ray petals could grow to a fixed length in gerbera species.

Genome-wide identification and characterization of the TIFY gene family in kiwifruit

Background

The TIFY gene family is a group of plant-specific transcription factors involved in regulation of plant growth and development and a variety of stress responses. However, the TIFY family has not yet been well characterized in kiwifruit, a popular fruit with important nutritional and economic value.

Results

A total of 27 and 21 TIFY genes were identified in the genomes of Actinidia eriantha and A. chinensis, respectively. Phylogenetic analyses showed that kiwifruit TIFY genes could be classified into four major groups, JAZ, ZML, TIFY and PPD, and the JAZ group could be further clustered into six subgroups (JAZ I to JAZ VI). Members within the same group or subgroup have similar exon-intron structures and conserved motif compositions. The kiwifruit TIFY genes are unevenly distributed on the chromosomes, and the segmental duplication events played a vital role in the expansion of the TIFY genes in kiwifruit. Syntenic analyses of TIFY genes between kiwifruit and other five plant species (including Arabidopsis thaliana, Camellia sinensis, Oryza sativa, Solanum lycopersicum and Vitis vinifera) and between the two kiwifruit species provided valuable clues for understanding the potential evolution of the kiwifruit TIFY family. Molecular evolutionary analysis showed that the evolution of kiwifruit TIFY genes was primarily constrained by intense purifying selection. Promoter cis-element analysis showed that most kiwifruit TIFY genes possess multiple cis-elements related to stress-response, phytohormone signal transduction and plant growth and development. The expression pattern analyses indicated that TIFY genes might play a role in different kiwifruit tissues, including fruit at specific development stages. In addition, several TIFY genes with high expression levels during Psa (Pseudomonas syringae pv. actinidiae) infection were identified, suggesting a role in the process of Pas infection.

Conclusions

In this study, the kiwifruit TIFY genes were identified from two assembled kiwifruit genomes. In addition, their basic physiochemical properties, chromosomal localization, phylogeny, gene structures and conserved motifs, synteny analyses, promoter cis-elements and expression patters were systematically examined. The results laid a foundation for further understanding the function of TIFY genes in kiwifruit, and provided a new potential approach for the prevention and treatment of Psa infection.

Supplementary Information

The online version contains supplementary material available at 10.1186/s12864-022-08398-8.

Transcriptomic Insight into Underground Floral Differentiation in Erythronium japonicum

Erythronium japonicum Decne (Liliaceae) flowers in early spring after overwintering. Its sexual reproduction process includes an underground development process of floral organs, but the underlying molecular mechanisms are obscure. The present study is aimed at exploring the transcriptional changes and key genes involved at underground floral developmental stages, including flower primordium differentiation, perianth differentiation, stamen differentiation, and pistil differentiation in E. japonicum. Multistage high-quality transcriptomic data resulted in identifying putative candidate genes for underground floral differentiation in E. japonicum. A total of 174,408 unigenes were identified, 28,508 of which were differentially expressed genes (DEGs) at different floral developmental stages, while only 44 genes were identified with conserved regulation between different stages. Further annotation of DEGs resulted in the identification of 270 DEGs specific to floral differentiation. In addition, ELF3, PHD, cullin 1, SE14, ZSWIM3, GIGNATEA, and SERPIN B were identified as potential candidate genes involved in the regulation of floral differentiation. Besides, we explored transcription factors with differential regulation at different developmental stages and identified bHLH, FAR1, mTERF, MYB-related, NAC, Tify, and WRKY TFs for their potential involvement in the underground floral differentiation process. Together, these results laid the foundation for future molecular works to improve our understanding of the underground floral differentiation process and its genetic regulation in E. japonicum.

The emerging role of jasmonate in the control of flowering time

Plants dynamically synchronize their flowering time with changes in the internal and external environments through a variety of signaling pathways to maximize fitness. In the last two decades, the major pathways associated with flowering, including the photoperiod, vernalization, age, autonomous, gibberellin, and ambient temperature pathways, have been extensively analyzed. In recent years, an increasing number of signals, such as sugar, thermosensory, stress, and certain hormones, have been shown to be involved in fine-tuning flowering time. Among these signals, the jasmonate signaling pathway has a function in the determination of flowering time that has not been systematically summarized. In this review, we present an overview of current knowledge of jasmonate control of flowering and discuss jasmonate crosstalk with other signals (such as gibberellin, defense, and touch) during floral transition.

Alternative splicing of the dormancy-associated MADS-box transcription factor gene PpDAM1 is associated with flower bud dormancy in 'Dangshansu' pear (Pyrus pyrifolia white pear group)

Alternative splicing (AS) plays a crucial role in plant growth, development and response to various environmental changes. However, whether alternative splicing of MADS-box transcription factors contributes to the flower bud dormancy process in fruit trees still remains unknown. In this work, the AS profile of genes in the dormant flower buds of 'Dangshansu' pear tree were examined. A total number of 3661 alternatively spliced genes were identified, and three mRNA isoforms of the dormancy associated MADS box (DAM) gene, PpDAM1, derived by alternative splicing, designated as PpDAM1.1, PpDAM1.2 and PpDAM1.3, were characterized. Bimolecular fluorescence complementation (BiFC) analysis indicated that AS of PpDAM1 didn't affect the nucleus localization and homo-/heterodimerization of PpDAM1.1, PpDAM1.2 and PpDAM1.3 proteins, but disturbed the translocation of PpDAM1.1/PpDAM1.1, PpDAM1.3/PpDAM1.3, PpDAM1.1/PpDAM1.3, and PpDAM1.2/PpDAM1.3 dimers to the nucleus. Constitutive expression of PpDAM1.2, but not PpDAM1.1 and PpDAM1.3, in Arabidopsis retarded the growth and development of transgenic plants. Further comparative expression analyses of PpDAM1.1, PpDAM1.2 and PpDAM1.3 in the flower buds of 'Dangshansu' and a less dormant pear cultivar, 'Cuiguan', exhibited that the expression of all the three isoforms in 'Dangshansu' were significantly higher than in 'Cuiguan', especially PpDAM1.2, which showed a predominantly higher expression than PpDAM1.1 and PpDAM1.3 in both cultivars. Our results suggest that alternative splicing of PpDAM1 could play a crucial role in pear flower bud dormancy process.

Morphological, Physiological, and Molecular Responses of Sweetly Fragrant Luculia gratissima During the Floral Transition Stage Induced by Short-Day Photoperiod

Photoperiod-regulated floral transition is vital to the flowering plant. Luculia gratissima "Xiangfei" is a flowering ornamental plant with high development potential economically and is a short-day woody perennial. However, the genetic regulation of short-day-induced floral transition in L. gratissima is unclear. To systematically research the responses of L. gratissima during this process, dynamic changes in morphology, physiology, and transcript levels were observed and identified in different developmental stages of long-day- and short-day-treated L. gratissima plants. We found that floral transition in L. gratissima occurred 10 d after short-day induction, but flower bud differentiation did not occur at any stage under long-day conditions. A total of 1,226 differentially expressed genes were identified, of which 146 genes were associated with flowering pathways of sugar, phytohormones, photoperiod, ambient temperature, and aging signals, as well as floral integrator and meristem identity genes. The trehalose-6-phosphate signal positively modulated floral transition by interacting with SQUAMOSA PROMOTER-BINDING-LIKE PROTEIN 4 (SPL4) in the aging pathway. Endogenous gibberellin, abscisic acid, cytokinin, and jasmonic acid promoted floral transition, whereas strigolactone inhibited it. In the photoperiod pathway, FD, CONSTANS-LIKE 12, and nuclear factors Y positively controlled floral transition, whereas PSEUDO-RESPONSE REGULATOR 7, FLAVIN-BINDING KELCH REPEAT F-BOX PROTEIN 1, and LUX negatively regulated it. SPL4 and pEARLI1 positively affected floral transition. Suppressor of Overexpression of Constans 1 and AGAMOUSLIKE24 integrated multiple flowering signals to modulate the expression of FRUITFULL/AGL8, AP1, LEAFY, SEPALLATAs, SHORT VEGETATIVE PHASE, and TERMINAL FLOWER 1, thereby regulating floral transition. Finally, we propose a regulatory network model for short-day-induced floral transition in L. gratissima. This study improves our understanding of flowering time regulation in L. gratissima and provides knowledge for its production and commercialization.

The transcription factor CmLEC1 positively regulates the seed-setting rate in hybridization breeding of chrysanthemum

Distant hybridization is widely used to develop crop cultivars, whereas the hybridization process of embryo abortion often severely reduces the sought-after breeding effect. The LEAFY COTYLEDON1 (LEC1) gene has been extensively investigated as a central regulator of seed development, but it is far less studied in crop hybridization breeding. Here we investigated the function and regulation mechanism of CmLEC1 from Chrysanthemum morifolium during its seed development in chrysanthemum hybridization. CmLEC1 encodes a nucleic protein and is specifically expressed in embryos. CmLEC1's overexpression significantly promoted the seed-setting rate of the cross, while the rate was significantly decreased in the amiR-CmLEC1 transgenic chrysanthemum. The RNA-Seq analysis of the developing hybrid embryos revealed that regulatory genes involved in seed development, namely, CmLEA (late embryogenesis abundant protein), CmOLE (oleosin), CmSSP (seed storage protein), and CmEM (embryonic protein), were upregulated in the OE (overexpressing) lines but downregulated in the amiR lines vs. wild-type lines. Future analysis demonstrated that CmLEC1 directly activated CmLEA expression and interacted with CmC3H, and this CmLEC1-CmC3H interaction could enhance the transactivation ability of CmLEC1 for the expression of CmLEA. Further, CmLEC1 was able to induce several other key genes related to embryo development. Taken together, our results show that CmLEC1 plays a positive role in the hybrid embryo development of chrysanthemum plants, which might involve activating CmLEA's expression and interacting with CmC3H. This may be a new pathway in the LEC1 regulatory network to promote seed development, one perhaps leading to a novel strategy to not only overcome embryo abortion during crop breeding but also increase the seed yield.

Transcriptome Analysis of Flower Development and Mining of Genes Related to Flowering Time in Tomato (Solanum lycopersicum)

Flowering is a morphogenetic process in which angiosperms shift from vegetative growth to reproductive growth. Flowering time has a strong influence on fruit growth, which is closely related to productivity. Therefore, research on crop flowering time is particularly important. To better understand the flowering period of the tomato, we performed transcriptome sequencing of early flower buds and flowers during the extension period in the later-flowering “Moneymaker” material and the earlier-flowering “20965” homozygous inbred line, and we analyzed the obtained data. At least 43.92 million clean reads were obtained from 12 datasets, and the similarity with the tomato internal reference genome was 92.86–94.57%. Based on gene expression and background annotations, 49 candidate genes related to flowering time and flower development were initially screened, among which the greatest number belong to the photoperiod pathway. According to the expression pattern of candidate genes, the cause of early flowering of “20965” is predicted. The modes of action of the differentially expressed genes were classified, and the results show that they are closely related to hormone regulation and participated in a variety of life activities in crops. The candidate genes we screened and the analysis of their expression patterns provide a basis for future functional verification, helping to explore the molecular mechanism of tomato flowering time more comprehensively.

Genome-Wide Association Studies for Sex Determination and Cross-Compatibility in Water Yam (Dioscorea alata L.)

Yam (Dioscorea spp.) species are predominantly dioecious, with male and female flowers borne on separate individuals. Cross-pollination is, therefore, essential for gene flow among and within yam species to achieve breeding objectives. Understanding genetic mechanisms underlying sex determination and cross-compatibility is crucial for planning a successful hybridization program. This study used the genome-wide association study (GWAS) approach for identifying genomic regions linked to sex and cross-compatibility in water yam (Dioscorea alata L.). We identified 54 markers linked to flower sex determination, among which 53 markers were on chromosome 6 and one on chromosome 11. Our result ascertained that D. alata is characterized by the male heterogametic sex determination system (XX/XY). The cross-compatibility indices, average crossability rate (ACR) and percentage high crossability (PHC), were controlled by loci on chromosomes 1, 6 and 17. Of the significant loci, SNPs located on chromosomes 1 and 17 were the most promising for ACR and PHC, respectively, and should be validated for use in D. alata hybridization activities to predict cross-compatibility success. A total of 61 putative gene/protein families with direct or indirect influence on plant reproduction were annotated in chromosomic regions controlling the target traits. This study provides valuable insights into the genetic control of D. alata sexual reproduction. It opens an avenue for developing genomic tools for predicting hybridization success in water yam breeding programs.