Genome-wide identification of auxin-responsive microRNAs in the poplar stem

Yang, Liguo; Ping, Tao; Lu, Wenjin; Song, Sangfa; Wang, Jianli; Wang, Qiao; Chai, Guohua; Bai, Youhuang; Chen, Yan

doi:10.1007/s13258-023-01385-7

Cited by 1 publication

(2 citation statements)

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“…Key regulators of auxin‐related epigenetic reprogramming are in the GRF family (Szczygieł‐Sommer & Gaj, 2019), members of which appear to be involved in recruitment of SWITCH/SUCROSE NONFERMENTING (SWI/SNF) chromatin remodeling complex (Debernardi et al ., 2014) and include our candidate Potri.002G115100 (homolog of GRF1 ). This poplar homolog is a likely target of a stem‐expressed microRNA transcriptionally regulated downstream of auxin (Yang et al ., 2023). In addition to acting both upstream (Szczygieł‐Sommer & Gaj, 2019) and downstream (Beltramino et al ., 2021; Yang et al ., 2023) of auxin, the GRF family has been implicated downstream of gibberellin signaling (van der Knaap et al ., 2000) and upstream of cytokinin, JA and SA, among other phytohormone pathways (Piya et al ., 2020).…”

Section: Discussionmentioning

confidence: 99%

“…This poplar homolog is a likely target of a stem‐expressed microRNA transcriptionally regulated downstream of auxin (Yang et al ., 2023). In addition to acting both upstream (Szczygieł‐Sommer & Gaj, 2019) and downstream (Beltramino et al ., 2021; Yang et al ., 2023) of auxin, the GRF family has been implicated downstream of gibberellin signaling (van der Knaap et al ., 2000) and upstream of cytokinin, JA and SA, among other phytohormone pathways (Piya et al ., 2020). A key role of GRF1 as a regeneration regulatory hub is supported by our epistasis results, showing significant interactions with 18 other candidates.…”

Section: Discussionmentioning

confidence: 99%

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Genome‐wide association study and network analysis of in vitro transformation in Populus trichocarpa support key roles of diverse phytohormone pathways and cross talk

Nagle,

Yuan,

Kaur

et al. 2024

New Phytologist

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Summary Wide variation in amenability to transformation and regeneration (TR) among many plant species and genotypes presents a challenge to the use of genetic engineering in research and breeding. To help understand the causes of this variation, we performed association mapping and network analysis using a population of 1204 wild trees of Populus trichocarpa (black cottonwood). To enable precise and high‐throughput phenotyping of callus and shoot TR, we developed a computer vision system that cross‐referenced complementary red, green, and blue (RGB) and fluorescent‐hyperspectral images. We performed association mapping using single‐marker and combined variant methods, followed by statistical tests for epistasis and integration of published multi‐omic datasets to identify likely regulatory hubs. We report 409 candidate genes implicated by associations within 5 kb of coding sequences, and epistasis tests implicated 81 of these candidate genes as regulators of one another. Gene ontology terms related to protein–protein interactions and transcriptional regulation are overrepresented, among others. In addition to auxin and cytokinin pathways long established as critical to TR, our results highlight the importance of stress and wounding pathways. Potential regulatory hubs of signaling within and across these pathways include GROWTH REGULATORY FACTOR 1 (GRF1), PHOSPHATIDYLINOSITOL 4‐KINASE β1 (PI‐4Kβ1), and OBF‐BINDING PROTEIN 1 (OBP1).

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