Gibberellins (GAs), enzymes that play a significant role in plant growth and development, and their levels in plants could be regulated by gibberellin-oxidases (GAoxs). As important fruit trees and ornamental plants, the study of the mechanism of plant architecture formation of the Prunus genus is crucial. Here, 85 GAox genes were identified from P. mume, P. armeniaca, P. salicina, and P. persica, and they were classified into six subgroups. Conserved motif and gene structure analysis showed that GAoxs were conserved in the four Prunus species. Collinearity analysis revealed two fragment replication events of PmGAoxs in the P. mume genome. Promoter cis-elements analysis revealed 24 PmGAoxs contained hormone-responsive elements and development regulatory elements. The expression profile indicated that PmGAoxs have tissue expression specificity, and GA levels during the dormancy stage of flower buds were controlled by certain PmGAoxs. After being treated with IAA or GA3, the transcription level of PmGA2ox8 in stems was significantly increased and showed a differential expression level between upright and weeping stems. GUS activity driven by PmGA2ox8 promoter was detected in roots, stems, leaves, and flower organs of Arabidopsis. PmGA2ox8 overexpression in Arabidopsis leads to dwarfing phenotype, increased number of rosette leaves but decreased leaf area, and delayed flowering. Our results showed that GAoxs were conserved in Prunus species, and PmGA2ox8 played an essential role in regulating plant height.

The optimal plant height is crucial in modern agriculture, influencing lodging resistance and facilitating mechanized crop production. Upland cotton (Gossypium hirsutum) is the most crucial fiber crop globally, but the knowledge of the genetic basis underlying plant height still needs to be discovered. Here we conducted a genome-wide association study (GWAS) to identify the major locus controlling plant height (PH1) in upland cotton. The locus encodes gibberellin 2-oxidase 1A (GhPH1), with a 1,133 bp-length structural variation (PAVPH1) located approximately 16 kb upstream of it. The presence or absence of PAVPH1 confers a differential expression of GhPH1, consequently leading to changes in plant height. Further analysis revealed that a gibberellin-regulating transcription factor (GhGARF) recognizes a specific \'CATTTG\' motif on the GhPH1 promoter and PAVPH1. This binding event down-regulates GhPH1, indicating that PAVPH1 functions as a distant upstream silencer. Intriguingly, we found that the critical repressor of the strigolactone (SL) signaling pathway, DWARF53 (D53), directly interacts with GhGARF and inhibits its binding to targets. Moreover, our study uncovers a previously unrecognized GA-SL crosstalk mechanism mediated by the GhD53-GhGARF-GhPH1/PAVPH1 module, crucial in regulating the plant height of upland cotton. These findings shed light on the genetic basis and gene interaction network underlying plant height and provide valuable insights for developing semi-dwarf cotton varieties through precise modulation of GhPH1 expression.

Plants NADP-malic enzymes (NADP-MEs) act as a class of oxidative decarboxylase to mediate malic acid metabolism in organisms. Despite NADP-MEs have been demonstrated to play pivotal roles in regulating diverse biological processes, the role of NADP-MEs involving in plant growth and development remains rarely known. Here, we characterized the function of rice cytosolic OsNADP-ME2 in regulating plant height. The results showed that RNAi silencing and knock-out of OsNADP-ME2 in rice results in a dwarf plant structure, associating with significant expression inhibition of genes involving in phytohormone Gibberellin (GA) biosynthesis and signaling transduction, but with up-regulation for the expression of GA signaling suppressor SLR1. The accumulation of major bioactive GA1, GA4 and GA7 are evidently altered in RNAi lines, and exogenous GA treatment compromises the dwarf phenotype of OsNADP-ME2 RNAi lines. RNAi silencing of OsNADP-ME2 also causes the reduction of NADP-ME activity associating with decreased production of pyruvate. Thus, our data revealed a novel function of plant NADP-MEs in modulation of rice plant height through regulating bioactive GAs accumulation and GA signaling, and provided a valuable gene resource for rice plant architecture improvement.

Plant height (PH) is a crucial trait for strengthening lodging resistance and boosting yield in foxtail millet. To identify quantitative trait loci (QTL) and candidate genes associated with PH, we first developed a genetic map using a recombinant inbred line (RIL) population derived from a cross between Aininghuang and Jingu 21. Then, PH phenotyping data and four variations of best linear unbiased prediction (BLUP) were collected from nine environments and three development stages. Next, QTL mapping was conducted using both unconditional and conditional QTL methods. Subsequently, candidate genes were predicted via transcriptome analysis of parental samples at three developmental stages. The results revealed that the genetic map, based on re-sequencing, consisted of 4,360 bin markers spanning 1,016.06 cM with an average genetic distance of 0.23 cM. A total of 19 unconditional QTL, accounting for 5.23%-35.36% of the phenotypic variation explained (PVE), which included 7 major and 4 stable QTL, were identified. Meanwhile, 13 conditional QTL, explaining 5.88%-40.35% of PVE, including 5 major and 3 stable QTL, were discovered. Furthermore, four consistent and stable QTL were identified. Finally, eight candidate genes were predicted through RNA-seq and weighted gene co-expression network analysis (WGCNA). Those findings provide a crucial foundation for understanding the genetic mechanisms underlying PH development and facilitate molecular marker-assisted breeding of ideal plant types in foxtail millet.

Wheat culms, comprising four to six internodes, are critically involved in determining plant height and lodging resistance, essential factors for field performance and regional adaptability. This study revealed the regulatory function of miR319 in common wheat plant height. Repression of tae-miR319 through short tandem target mimics (STTM) caused an increased plant height, while overexpression (OE) of tae-miR319 had the opposite effect. Overexpressing a miR319-resistant target gene TaPCF8 (rTaPCF8), increased plant height. TaPCF8 acted as a transcription repressor of downstream genes TaIAAs, which interact physically with TaSPL14. The significant differences of indole-3-acetic acid (IAA) contents indicate the involvement of auxin pathway in miR319-mediated plant height regulation. Finally, we identified two TaPCF8 haplotypes in global wheat collections. TaPCF8-5A-Hap2, as per association and evolution examinations, was subjected to strong substantial selection throughout wheat breeding. This haplotype, associated with shorter plant height, aligns with global breeding requirements. Consequently, in high-yield wheat breeding, we proposed a potential molecular marker for marker-assisted selection (MAS). Our findings offer fresh perspectives into the molecular mechanisms that underlie the miR319-TaPCF8 module\'s regulation of plant height by orchestrating auxin signaling and biosynthesis in wheat.

Ethylene response factors have been shown to be involved in the effects of plant developmental processes and to regulate stress tolerance. The aim of this study was to recognize the regulatory mechanisms of ethylene response factors on tobacco plant height. In this study, a gene-edited mutant (ERF10-KO) and wild type (WT) were utilized as experimental materials. Transcriptome and metabolome analyses were used to investigate the regulatory mechanism of NtERF10 gene editing on plant height in tobacco. Here, through the analysis of differentially expressed genes (DEGs), 2051 genes were upregulated and 1965 genes were downregulated. We characterized the different ERF10-KO and WT plant heights and identified key genes for photosynthesis, the plant hormone signal transduction pathway and the terpene biosynthesis pathway. NtERF10 was found to affect the growth and development of tobacco by regulating the expression levels of the PSAA, PSBA, GLY17 and GGP3 genes. Amino acid metabolism was analyzed by combining analyses of differentially expressed genes (DEGs) and differentially accumulated metabolites (DAMs). In addition, we found that members of the bHLH, NAC, MYB, and WRKY transcription factor families have vital roles in regulating plant height. This study not only provides important insights into the positive regulation of the ethylene response factor NtERF10 on plant height during plant growth and development but also provides new research ideas for tobacco molecular breeding.

We present a novel approach to genome-wide association studies (GWAS) by leveraging unstructured, spoken phenotypic descriptions to identify genomic regions associated with maize traits. Utilizing the Wisconsin Diversity panel, we collected spoken descriptions of Zea mays ssp. mays traits, converting these qualitative observations into quantitative data amenable to GWAS analysis. First, we determined that visually striking phenotypes could be detected from unstructured spoken phenotypic descriptions. Next, we developed two methods to process the same descriptions to derive the trait plant height, a well-characterized phenotypic feature in maize: (1) a semantic similarity metric that assigns a score based on the resemblance of each observation to the concept of \'tallness\' and (2) a manual scoring system that categorizes and assigns values to phrases related to plant height. Our analysis successfully corroborated known genomic associations and uncovered novel candidate genes potentially linked to plant height. Some of these genes are associated with gene ontology terms that suggest a plausible involvement in determining plant stature. This proof-of-concept demonstrates the viability of spoken phenotypic descriptions in GWAS and introduces a scalable framework for incorporating unstructured language data into genetic association studies. This methodology has the potential not only to enrich the phenotypic data used in GWAS and to enhance the discovery of genetic elements linked to complex traits but also to expand the repertoire of phenotype data collection methods available for use in the field environment.

Rice (Oryza sativa L.), a fundamental global staple, nourishes over half of the world\'s population. The identification of the ddt1 mutant in rice through EMS mutagenesis of the indica cultivar Shuhui527 revealed a dwarf phenotype, characterized by reduced plant height, smaller grain size, and decreased grain weight. Detailed phenotypic analysis and map-based cloning pinpointed the mutation to a single-base transversion in the LOC_Os03g04680 gene, encoding a cytochrome P450 enzyme, which results in a premature termination of the protein. Functional complementation tests confirmed LOC_Os03g04680 as the DDT1 gene responsible for the observed phenotype. We further demonstrated that the ddt1 mutation leads to significant alterations in gibberellic acid (GA) metabolism and signal transduction, evidenced by the differential expression of key GA-related genes such as OsGA20OX2, OsGA20OX3, and SLR1. The mutant also displayed enhanced drought tolerance, as indicated by higher survival rates, reduced water loss, and rapid stomatal closure under drought conditions. This increased drought resistance was linked to the mutant\'s improved antioxidant capacity, with elevated activities of antioxidant enzymes and higher expression levels of related genes. Our findings suggest that DDT1 plays a crucial role in regulating both plant height and drought stress responses. The potential for using gene editing of DDT1 to mitigate the dwarf phenotype while retaining improved drought resistance offers promising avenues for rice improvement.

The sunflower (Helianthus annuus L.) is one of the most essential oil crops in the world. Several component traits, including flowering time, plant height, stem diameter, seed weight, and kernel weight, determine sunflower seed and oil yield. Although the genetic mechanisms governing the variation of these yield-related traits have been studied using various approaches, genome-wide association studies (GWAS) have not been widely applied to sunflowers. In this study, a set of 342 sunflower accessions was evaluated in 2019 and 2020 using an incomplete randomized block design, and GWAS was conducted utilizing two complementary approaches: the mixed linear model (MLM) and the fixed and random model circulating probability unification (farmCPU) model by fitting 226,779 high-quality SNPs. As a result, GWAS identified a number of trait-associated SNPs. Those SNPs were located close to several genes that may serve as a basis for further molecular characterization and provide promising targets for sunflower yield improvement.

UNASSIGNED: Two economies of scale, predator satiation and pollination efficiency, have been proposed to explain the evolutionary mechanisms of mast seeding adopted by some long-lived plants. Plant height is strongly selected by pollination vectors and may also provide economies of scale; however, it remains unknown whether there is a close relationship between adult plant height and mast seeding intensity.
UNASSIGNED: Here, we analyzed mast seeding intensity of 158 plant species to test if adult plant height can select for mast seeding.
UNASSIGNED: We show that mast seeding intensities are higher in taller plant species irrespective of phylogeny, life form, pollination vector, and type of Spermatophytes. We also show that anemophily rather than entomophily selects for taller plant species and higher mast seeding intensities.
UNASSIGNED: The linear correlations and evolutionary links between adult plant height and mast seeding intensity provide evidence that mast seeding could have evolved as an adaptation to taller strategy of perennial plant species.