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.

The evolutionary analysis showed that the GF14 family was conserved, however, there was limited evidence linking GF14s to plant height. In our investigations, we discovered a co-expression relationship between ZmGF14s and functionally characterized genes linked to plant height. In the co-expression network, we identified ZmGF14-3, a gene expression exhibiting a positive correlation with plant height in three maize varieties, we postulated that this gene could be intimately linked to plant height development. Subsequently, we cloned ZmGF14-3 from the maize B73 inbred line and overexpressed it in Arabidopsis, resulting in markedly dwarfed transgenic phenotypes. Measurements of endogenous phytohormones disclosed a significant reduction in concentrations of Gibberellic Acid 7 (GA7) and Indole-3-Acetic Acid (IAA) in the overexpressed Arabidopsis, furthermore, qPCR results highlighted a pronounced decrease in the expression levels of plant height-related genes when compared to the wild type, therefore, it is plausible to posit that ZmGF14-3 plays a pivotal role in regulating the growth and development of maize through interactions with various phytohormone-related genes. Thus, delving into the potential interactions between ZmGF14-3 and these genes holds the promise of yielding valuable insights into the molecular mechanisms underpinning plant height development in maize.

BACKGROUND: Cassava is one of three major potato crops and the sixth most important food crop globally. Improving yield remains a primary aim in cassava breeding. Notably, plant height significantly impacts the yield and quality of crops; however, the mechanisms underlying cassava plant height development are yet to be elucidated.
RESULTS: In this study, we investigated the mechanisms responsible for cassava plant height development using phenotypic, anatomical, and transcriptomic analyses. Phenotypic and anatomical analysis revealed that compared to the high-stem cassava cultivar, the dwarf-stem cassava cultivar exhibited a significant reduction in plant height and a notable increase in internode tissue xylem area. Meanwhile, physiological analysis demonstrated that the lignin content of dwarf cassava was significantly higher than that of high cassava. Notably, transcriptome analysis of internode tissues identified several differentially expressed genes involved in cell wall synthesis and expansion, plant hormone signal transduction, phenylpropanoid biosynthesis, and flavonoid biosynthesis between the two cassava cultivars.
CONCLUSIONS: Our findings suggest that internode tissue cell division, secondary wall lignification, and hormone-related gene expression play important roles in cassava plant height development. Ultimately, this study provides new insights into the mechanisms of plant height morphogenesis in cassava and identifies candidate regulatory genes associated with plant height that can serve as valuable genetic resources for future crop dwarfing breeding.

Plant growth must be regulated throughout the plant life cycle. The myeloblastosis (MYB) transcription factor (TF) family is one of the largest TF families and is involved in metabolism, lignin biosynthesis, and developmental processes. Here, we showed that OsMYB14, a rice R2R3-MYB TF, was expressed in leaves and roots, especially in rice culm and panicles, and that it localized to the nucleus. Overexpression of OsMYB14 (OsMYB14-ox) in rice resulted in a 30% reduction in plant height compared to that of the wild type (WT), while the height of the osmyb14-knockout (osmyb14-ko) mutant generated using the CRISPR/Cas9 system was not significantly different. Microscopic observations of the first internode revealed that the cell size did not differ significantly among the lines. RNA sequencing analysis revealed that genes associated with plant development, regulation, lipid metabolism, carbohydrate metabolism, and gibberellin (GA) and auxin metabolic processes were downregulated in the OsMYB14-ox line. Hormone quantitation revealed that inactive GA19 accumulated in OsMYB14-ox but not in the WT or knockout plants, suggesting that GA20 generation was repressed. Indole-3-acetic acid (IAA) and IAA-aspartate accumulated in OsMYB14-ox and osmyb14-ko, respectively. Indeed, real-time PCR analysis revealed that the expression of OsGA20ox1, encoding GA20 oxidase 1, and OsGH3-2, encoding IAA-amido synthetase, was downregulated in OsMYB14-ox and upregulated in osmyb14-ko. A protein-binding microarray revealed the presence of a consensus DNA-binding sequence, the ACCTACC-like motif, in the promoters of the OsGA20ox1 and GA20ox2 genes. These results suggest that OsMYB14 may act as a negative regulator of biological processes affecting plant height in rice by regulating GA biosynthesis and auxin metabolism.