Integration of photoperiod signaling with other

The gap

Evidence profile

Stated in the future work and conclusions sections of the source papers, classified as general, spanning 4 journals. Those papers have been cited 1 times in total.

Supporting evidence — 4 representative gaps

• Genome evolution through polyploidy: Enhancing plant stress resilience in agriculture (2026) · Proceedings of the National Academy of Sciences · cited 1× · doi

  Polyploidy is now understood to drive significant shifts in gene content and cis-regulatory variation, both of which are fundamental to plant stress resilience. Gene content variation, including the gain or loss of specific genes, directly impacts metabolic and signaling pathways vital for adapting to environmental challenges. Simultaneously, changes in CREs lead to diverse and novel patterns of gene activity that fine-tune stress responses. This dynamic interplay between genetic and regulatory changes contributes to the expanded phenotypic diversity and enhanced adaptive capabilities that enable polyploids to thrive under challenging conditions. A comprehensive understanding of regulatory variation in polyploids holds immense potential for developing nextgeneration, climate-resilient crops and ensuring global food security. While the added phenotypic diversity, genetic Fig. 4. HE and its impact on gene dosage and structure. This figure illustrates how HEs, which are recombination events between chromosomes from different diploid progenitors (shown in blue and yellow), can alter gene dosage and create novel gene structures in a polyploid genome. Panel (A) depicts the potential outcomes of HE on homoeolog dosage. A newly formed tetraploid begins with two copies from each parental genome (Left). HEs and subsequent segregation can alter this ratio to 3:1 or 1:3 (Middle) and, in extreme cases, to 4:0 or 0:4 (Right). Panel (B) shows that HEs can also occur within a gene. These events can either alter CRE variants associated with a gene (Left to Middle) or, in more extreme cases, create chimeric versions of genes consisting of exons from both homoeologs (Middle to Right). 8 of 10 https://doi.org/10.1073/pnas.2522064123 pnas.org redundancy, and multiple gene variants in polyploids provide a rich substrate for adaptation, they have historically made it difficult to apply molecular breeding approaches. For this reason, some breeding communities have opted to work with diploid progenitors, sacrificing valuable phenotypic diversity for the simplicity and lower cost of genetic markers. The advent of new genotyping and bioinformatic tools, combined with the development of haplotype-phased pangenomes, is making the use of molecular breeding tools with polyploids increasingly more accessible and affordable for a broader range of communities working on a wide variety of polyploid crops. While significant progress has been made in understanding gene and CRE evolution following polyploidy, many aspects remain poorly understood. It is likely that insights into stress adaptations and resilience are likely to derive from these five key research areas. 1 Dissecting Regulatory Complexes: Understanding which CREs function together to regulate a single gene is a major challenge.

  generalstated in future workevidence 5/5
  Keywords: gene regulatory polyploids stress genetic phenotypic diversity dosage alter middle breeding polyploidy understood significant content
• Comparative Chloroplast Genomics of Sugar Beet and Wild Relatives: Insights into Photosystem Gene Regulation and Stress Tolerance (2026) · Functional & Integrative Genomics · doi

  These findings provide valuable insights for applied breed- ing programs. Identification of SNP differences and varia- tions within promoter regions of PSI and PSII genes may be particularly relevant for studies on climate resilience. Although gene expression analysis was not performed in the present study, future investigations incorporating in-depth molecular analyses will be essential to elucidate the regula- tory effects of SNPs and indels within promoter fragments and their contribution to stress-responsive gene regulation. In conclusion, the promoter regions of chloroplast- encoded photosystem genes in Beta exhibit a highly conserved regulatory architecture characterized by the coordinated presence of PEP and NEP elements. This dual- promoter framework likely ensures robust and flexible tran- scriptional control under varying environmental conditions. While overall sequence conservation reflects strong evo- lutionary constraint, the presence of minor SNPs, particu- larly in B. corolliflora, highlights subtle genetic variation that may contribute to adaptive regulation rather than major functional divergence. Together, these findings suggest that Beta chloroplast promoters are finely tuned to balance transcriptional stabil- ity with limited regulatory plasticity, providing a molecular basis for maintaining photosynthetic efficiency and resil- ience under abiotic stress. These insights offer a foundation for exploiting promoter variation in future breeding strate- gies aimed at improving stress tolerance in sugar beet. Future research should prioritize three key directions to translate these genomic insights into practical applications. Page 15 of 18 98 First, functional validation of identified cis-elements through expression profiling under controlled stress conditions, pro- moter–reporter assays, and transgenic analyses will con- firm their regulatory roles and stress-response mechanisms. Second, the integration of chloroplast genomic insights with advanced gene-editing technologies, such as CRISPR- based promoter modification, offers a promising approach to fine-tune photosystem gene regulation and improve plant performance under climate-induced stress without introduc- ing foreign DNA. Third, expanding chloroplast comparative studies across a wider range of Beta accessions, including underutilized wild populations and landraces, will further elucidate the molecular mechanisms underlying stress resil- ience and uncover additional genetic diversity for breeding. Together, these efforts will guide the development of high- yielding, climate-resilient sugar beet cultivars for sustain- able agriculture in the face of global environmental change. Supplementary Information The online version contains supplementary material available at h t t p s : / / d o i . o r g / 1 0 . 1 0 0 7 / s 1 0 1 4 2 - 0 2 6 - 0 1 8 8 3 - 3 . Acknowledgements Noreen Aslam is thankful to TUBITAK for sup- porting her studies. Mehmet Örgeç was supported by the TÜBİTAK Scientist Support Programs Directorate (BİDEB), 2211-A National PhD Scholarship Program, and The Higher Education Council (YÖK) through 100/2000 Doctoral Scholarship Program. Author contributions Conceptualization: MS, MTW and SG. Method- ology: MS, MTW and MCB. Formal analysis and investigation: MS, Abdullah, NB, IA, MCB, NA, MO, MTW, EG and SG. Writing - origi- nal draft preparation: Abdullah, MS, NA, MTW and SG. Writing - re- view and editing: MS, Abdullah, MTW, MCB, NA, MO, EG and SG. Funding acquisition: SG. Resources: IA, MTW, and SG. Supervision: MTW and SG. Funding This work was supported by Scientific and Technological Re- search Council of Türkiye (TÜBİTAK) (Grant No. KBAG-120O596) to Songul Gurel. Data availability The sequencing data of the sugar beet genotypes were deposited to NCBI under the accession numbers PV151546 PV069735, PV069737, PV069736, PV135462, PV135457, PV135461, PV135459, PV135458, PV135460.

  generalstated in future workevidence 5/5
  Keywords: stress promoter insights gene chloroplast climate future molecular regulation beta regulatory sugar beet abdullah programs
• Cytokinin availability and chloroplast functional lifetime in senescing leaves (2026) · Frontiers in Plant Science · doi

  Evidence from Arabidopsis and other systems indicates that CK signaling delays chlorophyll catabolism, slows disassembly of photosynthetic complexes, supports chloroplast-related gene expression, and limits ROS-driven acceleration of senescence. The recent observation in detached Arabidopsis leaves that CKs can transiently and reversibly downregulate PSII photochemistry during prolonged darkness adds an important nuance. In such contexts, CK action may protect leaves by lowering electron pressure and improving redox control before later photosynthetic competence is maintained, indicating that transient photosynthetic down-modulation can be part of the protective response (Krieger‐Liszkay et al., 2019; Domı́nguez and Cejudo, 2021; Kábrtová et al., 2026). Several lines of evidence indicate that CKs actively reprogram the transcriptome of mature leaves and buffer redox-dependent feedbacks associated with photosynthetic decline.

  generalstated in future workevidence 5/5
  Keywords: leaves photosynthetic evidence arabidopsis redox systems indicates signaling delays chlorophyll catabolism slows disassembly tosynthetic complexes
• Genetic Regulation of Photoperiod Sensitivity in Flowering Plants (2026) · Zenodo (CERN European Organization for Nuclear Research) · doi

  Additionally, integration of photoperiod signaling with other environmental response pathways, particularly those involving temperature and water availability, remains incompletely understood and deserves further investigation to develop crops resilient to multiple environmental stresses.

  generalstated in conclusionsevidence 5/5
  Keywords: environmental additionally integration photoperiod signaling response pathways particularly involving temperature water availability remains incompletely understood

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