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1. LEAFY is a pioneer transcription factor and licenses cell reprogramming to floral fate

   https://doi.org/10.1038/s41467-020-20883-w  

   Jin, Run; Klasfeld, Samantha; Zhu, Yang; Fernandez Garcia, Meilin; Xiao, Jun; Han, Soon-Ki; Konkol, Adam; Wagner, Doris (December 2021, Nature Communications)

   null (Ed.)

   Abstract Master transcription factors reprogram cell fate in multicellular eukaryotes. Pioneer transcription factors have prominent roles in this process because of their ability to contact their cognate binding motifs in closed chromatin. Reprogramming is pervasive in plants, whose development is plastic and tuned by the environment, yet little is known about pioneer transcription factors in this kingdom. Here, we show that the master transcription factor LEAFY (LFY), which promotes floral fate through upregulation of the floral commitment factor APETALA1 ( AP1 ), is a pioneer transcription factor. In vitro, LFY binds to the endogenous AP1 target locus DNA assembled into a nucleosome. In vivo, LFY associates with nucleosome occupied binding sites at the majority of its target loci, including AP1 . Upon binding, LFY ‘unlocks’ chromatin locally by displacing the H1 linker histone and by recruiting SWI/SNF chromatin remodelers, but broad changes in chromatin accessibility occur later. Our study provides a mechanistic framework for patterning of inflorescence architecture and uncovers striking similarities between LFY and animal pioneer transcription factor. 

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2. Florigen-producing cells express FPF1-LIKE PROTEIN 1 that accelerates flowering and stem growth in long days with sunlight red/far-red ratio in Arabidopsis

   https://doi.org/10.1101/2024.04.26.591289  

   Takagi, Hiroshi; Lee, Nayoung; Hempton, Andrew K; Purushwani, Savita; Notaguchi, Michitaka; Yamauchi, Kota; Shirai, Kazumasa; Kawakatsu, Yaichi; Uehara, Susumu; Albers, William G; et al (April 2024, bioRxiv)

   Summary Seasonal changes in spring induce flowering by expressing the florigen, FLOWERING LOCUS T (FT), inArabidopsis.FTis expressed in unique phloem companion cells with unknown characteristics. The question of which genes are co-expressed withFTand whether they have roles in flowering remains elusive. Through tissue-specific translatome analysis, we discovered that under long-day conditions with the natural sunlight red/far-red ratio, theFT-producing cells express a gene encoding FPF1-LIKE PROTEIN 1 (FLP1). The masterFTregulator, CONSTANS (CO), controlsFLP1expression, suggestingFLP1’s involvement in the photoperiod pathway. FLP1 promotes early flowering independently ofFT,is active in the shoot apical meristem, and induces the expression ofSEPALLATA 3(SEP3), a key E-class homeotic gene. Unlike FT, FLP1 facilitates inflorescence stem elongation. Our cumulative evidence indicates that FLP1 may act as a mobile signal. Thus, FLP1 orchestrates floral initiation together with FT and promotes inflorescence stem elongation during reproductive transitions. 

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3. LEAFY demonstrates functions in reproductive development of the gametophyte but not the sporophyte of the fern Ceratopteris richardii

   https://doi.org/10.1242/dev.204808  

   McConnell, Hannah; Lanclos, Jancee_R; Willis, Katelynn; Gjording, Nicholas; Stockmann, Genevieve; Lind, Catalina; Maloof, Julin_N; Plackett, Andrew_R_G; Di_Stilio, Verónica_S (November 2025, Development)

   Flowers are a key reproductive innovation of the angiosperms. Seed plant reproductive axes (including flowers) evolved as reproductively specialized shoots of the land plant diploid sporophyte, with the gamete-producing haploid gametophyte becoming reduced and enclosed within ovules and microsporangia. The transcription factor LEAFY (LFY) initiates floral development, yet it predates flowers and is found across all land plants. LFY function outside angiosperms is known from the moss Physcomitrium patens, where it controls the first cell division of the sporophyte, and from the model fern Ceratopteris richardii, a seedless vascular plant where CrLFY1 and CrLFY2 maintain vegetative meristem activity. However, how LFY’s floral role evolved remains unclear. Using over-expression, we uncover new roles for CrLFY1/2 in fern gametophyte reproduction, in sperm cells and in the gametophyte's multicellular notch meristem. While no sporophytic reproductive function was detected in terms of time to sporing, over-expression supports a role in frond compounding and in the zygote's first cell division. Our findings suggest a potentially ancestral LFY function in fern haploid-stage reproduction, which might have been co-opted into the sporophyte during the origin of the flower. 

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4. An ethylene biosynthesis enzyme controls quantitative variation in maize ear length and kernel yield

   https://doi.org/10.1038/s41467-021-26123-z  

   Ning, Qiang; Jian, Yinan; Du, Yanfang; Li, Yunfu; Shen, Xiaomeng; Jia, Haitao; Zhao, Ran; Zhan, Jimin; Yang, Fang; Jackson, David; et al (October 2021, Nature Communications)

   Abstract Maize ear size and kernel number differ among lines, however, little is known about the molecular basis of ear length and its impact on kernel number. Here, we characterize a quantitative trait locus,qEL7, to identify a maize gene controlling ear length, flower number and fertility.qEL7encodes 1-aminocyclopropane-1- carboxylate oxidase2 (ACO2), a gene that functions in the final step of ethylene biosynthesis and is expressed in specific domains in developing inflorescences. Confirmation ofqEL7by gene editing ofZmACO2leads to a reduction in ethylene production in developing ears, and promotes meristem and flower development, resulting in a ~13.4% increase in grain yield per ear in hybrids lines. Our findings suggest that ethylene serves as a key signal in inflorescence development, affecting spikelet number, floral fertility, ear length and kernel number, and also provide a tool to improve grain productivity by optimizing ethylene levels in maize or in other cereals. 

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5. Cryptic variation fuels plant phenotypic change through hierarchical epistasis

   https://doi.org/10.1038/s41586-025-09243-0  

   Zebell, Sophia G; Martí-Gómez, Carlos; Fitzgerald, Blaine; Cunha, Camila P; Lach, Michael; Seman, Brooke M; Hendelman, Anat; Sretenovic, Simon; Qi, Yiping; Bartlett, Madelaine; et al (July 2025, Nature)

   Abstract Cryptic genetic variants exert minimal phenotypic effects alone but are hypothesized to form a vast reservoir of genetic diversity driving trait evolvability through epistatic interactions^1–3. This classical theory has been reinvigorated by pan-genomics, which is revealing pervasive variation within gene families,cis-regulatory regions and regulatory networks^4–6. Testing the ability of cryptic variation to fuel phenotypic diversification has been hindered by intractable genetics, limited allelic diversity and inadequate phenotypic resolution. Here, guided by natural and engineeredcis-regulatory cryptic variants in a paralogous gene pair, we identified additional redundanttransregulators, establishing a regulatory network controlling tomato inflorescence architecture. By combining coding mutations withcis-regulatory alleles in populations segregating for all four network genes, we generated 216 genotypes spanning a wide spectrum of inflorescence complexity and quantified branching in over 35,000 inflorescences. Analysis of this high-resolution genotype–phenotype map using a hierarchical model of epistasis revealed a layer of dose-dependent interactions within paralogue pairs enhancing branching, culminating in strong, synergistic effects. However, we also identified a layer of antagonism between paralogue pairs, whereby accumulating mutations in one pair progressively diminished the effects of mutations in the other. Our results demonstrate how gene regulatory network architecture and complex dosage effects from paralogue diversification converge to shape phenotypic space, producing the potential for both strongly buffered phenotypes and sudden bursts of phenotypic change. 

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