Pineapple (Ananas comosus var. comosus) and ornamental bromeliads are commercially induced to flower by treatment with ethylene or its analogs. The apex is transformed from a vegetative to a floral meristem and shows morphological changes in 8 to 10 days, with flowers developing 8 to 10 weeks later. During eight sampling stages ranging from 6 h to 8 days after treatment, 7961 genes were found to exhibit differential expression (DE) after the application of ethylene. In the first 3 days after treatment, there was little change in ethylene synthesis or in the early stages of the ethylene response. Subsequently, three ethylene response transcription factors (ERTF) were up‐regulated and the potential gene targets were predicted to be the positive flowering regulator CONSTANS‐like 3 (CO), a WUSCHEL gene, two APETALA1/FRUITFULL (AP1/FUL) genes, an epidermal patterning gene, and a jasmonic acid synthesis gene. We confirm that pineapple has lost the flowering repressor FLOWERING LOCUS C. At the initial stages, the SUPPRESSOR OF OVEREXPRESSION OF CONSTANS 1 (SOC1) was not significantly involved in this transition. Another WUSCHEL gene and a PHD homeobox transcription factor, though not apparent direct targets of ERTF, were up‐regulated within a day of treatment, their predicted targets being the up‐regulated CO, auxin response factors, SQUAMOSA, and histone H3 genes with suppression of abscisic acid response genes. The FLOWERING LOCUS T (FT), TERMINAL FLOWER (TFL), AGAMOUS‐like APETELAR (AP2), and SEPETALA (SEP) increased rapidly within 2 to 3 days after ethylene treatment. Two FT genes were up‐regulated at the apex and not at the leaf bases after treatment, suggesting that transport did not occur. These results indicated that the ethylene response in pineapple and possibly most bromeliads act directly to promote the vegetative to flower transition via APETALA1/FRUITFULL (AP1/FUL) and its interaction with SPL, FT, TFL, SEP, and AP2. A model based on AP2/ERTF DE and predicted DE target genes was developed to give focus to future research. The identified candidate genes are potential targets for genetic manipulation to determine their molecular role in flower transition.

Background: Diseases are the major factor affecting the quality and yield of sugarcane during its growth and development. However, our knowledge about the factors regulating disease responses remain limited. The present study focuses on identifying genes regulating transcriptional mechanisms responsible for resistance to leaf scald caused by Xanthomonas albilineans in S. spontaneum and S. officinarum. Results: After inoculation of the two sugarcane varieties SES208 (S. spontaneum) and LA Purple (S. officinarum) with Xanthomonas albilineans, SES208 exhibited significantly greater resistance to leaf scald caused by X. albilineans than did LA Purple. Using transcriptome analysis, we identified a total of 4323 and 1755 differentially expressed genes (DEGs) in inoculated samples of SES208 and LA Purple, respectively. Significantly, 262 DEGs were specifically identified in SES208 that were enriched for KEGG pathway terms such as plant-pathogen interaction, MAPK signaling pathway, and plant hormone signal transduction. Furthermore, we built a transcriptional regulatory co-expression network that specifically identified 16 and 25 hub genes in SES208 that were enriched for putative functions in plant-pathogen interactions, MAPK signaling, and plant hormone signal transduction. All of these essential genes might be significantly involved in resistance-regulating responses in SES208 after X. albilineans inoculation. In addition, we found allele-specific expression in SES208 that was associated with the resistance phenotype of SES208 when infected by X. albilineans. After infection with X. albilineans, a great number of DEGs associated with the KEGG pathways ‘phenylpropanoid biosynthesis’ and ‘flavonoid biosynthesis’ exhibited significant expression changes in SES208 compared to LA Purple that might contribute to superior leaf scald resistance in SES208. Conclusions: We provided the first systematical transcriptome map that the higher resistance of SES208 is associated with and elicited by the rapid activation of multiple clusters of defense response genes after infection by X. albilineans and not merely due to changes in the expression of genes generically associated with stress resistance. These results will serve as the foundation for further understanding of the molecular mechanisms of resistance against X. albilineans in S. spontaneum.

Papaya exhibits three sex types: female (XX), male (XY), and hermaphrodite (XYh), making it an unusual trioecious model for studying sex determination. A critical aspect of papaya sex determination is the pistil abortion in male flowers. However, the regulatory networks that control the development of pistils and stamens in papaya remain incompletely understood. In this study, we identified three organ-specific clusters involved in papaya pistils and stamens development. We found that pistil development is primarily characterized by the significant expression of auxin-related genes, while the pistil abortion genes in males is mainly associated with cytokinin, gibberellin, and auxin pathways. Additionally, we constructed expression regulatory networks for the development of female pistils, aborted pistils and stamens in male flowers, revealing key regulatory genes and signaling pathways involved in papaya organ development. Furthermore, we systematically identified 65 members of the MADS-box gene family and 10 ABCDE subfamily MADS-box genes in papaya. By constructing a phylogenetic tree of the ABCDE subfamily, we uncovered gene contraction and expansion in papaya, providing an improved understanding of the developmental mechanisms and evolutionary history of papaya floral organs. These findings provide a robust framework for identifying candidate sex-determining genes and constructing the sex determination regulatory network in papaya, providing insights and genomic resources for papaya breeding.

Papaya is a major tropical fruit crop with notable nutritional and economic value, yet its genetic improvement through modern breeding technologies faces substantial challenges. The traditional tissue culture process is both labor-intensive and time-consuming, causing gene-editing advancements in papaya to lag behind those in other crops. To overcome these obstacles, we developed a tissue culture–independent hairy root system in papaya, which enables efficient gene editing and significantly enhances the application and development of editing tools. This innovative platform allows for the pre-assessment of editing efficiency and supports the establishment of adenine base editor (ABE) and cytosine base editor (CBE) tools in papaya, thereby mitigating the high failure costs associated with the lengthy cycle of conventional genetic transformation. Utilizing this system, we pre-tested sgRNA activity and achieved high editing efficiency of CpWIP3 during stable transformation. Additionally, through promoter screening, we successfully developed ABE and CBE tools, marking the first precise single-nucleotide editing system in papaya. This gene-editing system provides a crucial platform for advancing functional genomics and accelerating precision breeding in papaya.

Papayas possess three sex genotypes: female XX, male XY, and hermaphrodite XY^h. Only male plants produce long peduncles with numerous flowers, a trait that improves reproductive success. The gene SHORT VEGETATIVE PHASE (CpSVP) is located on the Y chromosome, absent from the X chromosome, and disrupted in the Y^h chromosome, making it a key candidate gene for long peduncles in male plants. An autosomal CpSVP allele (CpSVP-A) was also annotated in a papaya genome. The overexpression of the male allele in Arabidopsis increases pedicel length, which supports its role in pedicel elongation. Unexpectedly, the autosomal allele CpSVP-A produced a similar phenotype as the male one, while the hermaphroditic allele (CpSVP-Y^h) did not cause any significant change in pedicel length. Additionally, only the male allele rescued early flowering in an Atsvp mutant, indicating that it regulates both pedicel length and flowering time. In contrast, the autosomal allele only affected pedicel elongation and had no effect on flowering time. Together, these results demonstrate that CpSVP-Y underwent subfunctionalization, retaining both peduncle elongation and flowering time functions, while CpSVP-A likely lost the latter. Thus, CpSVP-Y contributes to male reproductive fitness through enhanced peduncle development without affecting sex determination, potentially regulated by Y chromosome-specific cis-elements. This study provides new insights into the genetic basis of sexually dimorphic traits in papayas.