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The calmodulin-binding protein 60 (CBP60) family is a gene family unique to plants, and its members play a crucial role in plant defense responses to pathogens and growth and development. Considering that cotton is the primary source of natural cotton textile fiber, the functional study of its CBP60 gene family members is critical. In this research, we successfully identified 162 CBP60 members from the genomes of 21 species. Of these, 72 members were found in four cotton species, divided into four clades. To understand the function of GhCBP60B in cotton in depth, we conducted a detailed analysis of its sequence, structure, cis-acting elements, and expression patterns. Research results show that GhCBP60B is located in the nucleus and plays a crucial role in cotton growth and development and response to salt and drought stress. After using VIGS (virus-induced gene silencing) technology to conduct gene silencing experiments, we found that the plants silenced by GhCBP60B showed dwarf plants and shortened stem nodes, and the expression of related immune genes also changed. In further abiotic stress treatment experiments, we found that GhCBP60B-silenced plants were more sensitive to drought and salt stress, and their POD (peroxidase) activity was also significantly reduced. These results imply the vital role of GhCBP60B in cotton, especially in regulating plant responses to drought and salt stress. This study systematically analyzed CBP60 gene family members through bioinformatics methods and explored in depth the biological function of GhCBP60B in cotton. These research results lay a solid foundation for the future use of the GhCBP60B gene to improve cotton plant type and its drought and salt resistance. [ABSTRACT FROM AUTHOR]

The YABBY gene family plays an important role in plant growth and development, such as response to abiotic stress and lateral organ development. YABBY TFs are well studied in numerous plant species, but no study has performed a genome-wide investigation of the YABBY gene family in Melastoma dodecandrum. Therefore, a genome-wide comparative analysis of the YABBY gene family was performed to study their sequence structures, cis-acting elements, phylogenetics, expression, chromosome locations, collinearity analysis, protein interaction, and subcellular localization analysis. A total of nine YABBY genes were found, and they were further divided into four subgroups based on the phylogenetic tree. The genes in the same clade of phylogenetic tree had the same structure. The cis-element analysis showed that MdYABBY genes were involved in various biological processes, such as cell cycle regulation, meristem expression, responses to low temperature, and hormone signaling. MdYABBYs were unevenly distributed on chromosomes. The transcriptomic data and real-time reverse transcription quantitative PCR (RT-qPCR) expression pattern analyses showed that MdYABBY genes were involved in organ development and differentiation of M. dodecandrum, and some MdYABBYs in the subfamily may have function differentiation. The RT-qPCR analysis showed high expression of flower bud and medium flower. Moreover, all MdYABBYs were localized in the nucleus. Therefore, this study provides a theoretical basis for the functional analysis of YABBY genes in M. dodecandrum. [ABSTRACT FROM AUTHOR]

Helicoverpa armigera is a polyphagous destructive lepidopteran pest with strong Bacillus thuringiensis (Bt) resistance. Cholesterol, a vital component for insect growth, can only be obtained from food, and its transfer and metabolism are regulated by sterol carrier protein-2 (SCP-2). This study examined whether H. armigera SCP-2 (HaSCP-2) gene expression, involved in cholesterol absorption, can be silenced by nanocarrier fluorescent nanoparticle-RNA interference (FNP-RNAi) by larval feeding and whether the silencing affected H. armigera development. Fluorescence microscopy showed that nanoparticle-siRNA was distributed in Ha cells and the larval midgut. FNP-HaSCP-2 siRNA suppressed HaSCP-2 expression by 52.5% in H.armigera Ha cells. FNP can effectively help deliver siRNA into cells, protect siRNA, and is not affected by serum. FNP-siRNA in vivo biological assays showed that HaSCP-2 transcript levels were inhibited by 70.19%, 68.16%, and 67.66% in 3rd, 4th, and 5th instar larvae, leading to a decrease in the cholesterol level in the larval and prepupal fatbodies. The pupation rate and adult emergence were reduced to 26.0% and 56.52%, respectively. This study demonstrated that FNP could deliver siRNA to cells and improve siRNA knockdown efficiency. HaSCP-2 knockdown by FNP-siRNA in vivo hindered H. armigera growth and development. FNP could enhance RNAi efficiency to achieve pest control by SCP-2-targeted FNP-RNAi. [ABSTRACT FROM AUTHOR]

Growth-regulating factor (GRF) is a kind of transcription factor unique to plants, playing an important role in the flowering regulation, growth, and development of plants. Melastoma dodecandrum is an important member of Melastomataceae, with ornamental, medicinal, and edible benefits. The identification of the GRF gene family in M. dodecandrum can help to improve their character of flavor and continuous flowering. The members of the GRF gene family were identified from the M. dodecandrum genome, and their bioinformatics, selective pressure, and expression patterns were analyzed. The results showed that there were 20 GRF genes in M. dodecandrum. Phylogenetic analysis showed that the 71 GRF genes from M. dodecandrum, Arabidopsis thaliana, Camellia sinensis, and Oryza sativa can be divided into three clades and six subclades. The 20 GRF genes of M. dodecandrum were distributed in twelve chromosomes and one contig. Furthermore, the gene structure and motif analysis showed that the intron and motif within each clade were very similar, but there were great differences among different clades. The promoter contained cis-acting elements related to hormone induction, stress, and growth and development. Different transcriptomic expression of MdGRFs indicated that MdGRFs may be involved in regulating the growth and development of M. dodecandrum. The results laid a foundation for further study on the function and molecular mechanism of the M. dodecandrum GRF gene family. [ABSTRACT FROM AUTHOR]

Simple Summary: The GRAS gene family plays a critical role in regulation of growth, defense, light and hormone responses. We identified 45 GRAS genes in the pitaya genome and categorized them into nine respective subfamilies: PAT1, SHR, LISCL, HAM, SCR, RGL, LAS, DELLA and SCL-3. Among these 45 HuGRAS family members, we reported nine candidate genes that played key roles in the growth and development of the pitaya plant. The GRAS gene family is one of the most important families of transcriptional factors that have diverse functions in plant growth and developmental processes including axillary meristem patterning, signal-transduction, cell maintenance, phytohormone and light signaling. Despite their importance, the function of GRAS genes in pitaya fruit (Selenicereus undatus L.) remains unknown. Here, 45 members of the HuGRAS gene family were identified in the pitaya genome, which was distributed on 11 chromosomes. All 45 members of HuGRAS were grouped into nine subfamilies using phylogenetic analysis with six other species: maize, rice, soybeans, tomatoes, Medicago truncatula and Arabidopsis. Among the 45 genes, 12 genes were selected from RNA-Seq data due to their higher expression in different plant tissues of pitaya. In order to verify the RNA-Seq data, these 12 HuGRAS genes were subjected for qRT-PCR validation. Nine HuGRAS genes exhibited higher relative expression in different tissues of the plant. These nine genes which were categorized into six subfamilies inlcuding DELLA (HuGRAS-1), SCL-3 (HuGRAS-7), PAT1 (HuGRAS-34, HuGRAS-35, HuGRAS-41), HAM (HuGRAS-37), SCR (HuGRAS-12) and LISCL (HuGRAS-18, HuGRAS-25) might regulate growth and development in the pitaya plant. The results of the present study provide valuable information to improve tropical pitaya through a molecular and conventional breeding program. [ABSTRACT FROM AUTHOR]

Sugar Will Eventually be Exported Transporters (SWEET) proteins function as sugar transporters that play key roles in plant growth, development, and biotic and abiotic stress responses. However, little is known about the SWEET gene family in common bean (Phaseolus vulgaris L.). In this study, 24 putative PvSWEET genes were identified. They can be categorized into four subgroups based on a phylogenetic analysis, exon–intron structure, cis-regulatory elements, and MEME motifs. A collinearity analysis showed that three pairs of segmental duplicated events were identified. The Phytozome database showed that 16 PvSWEET genes were highly expressed in reproductive organs. PvSWEET5 was expressed the most highly in all the tissues tested, while PvSWEET8/9/10/13 were undetectable in the datasets. The results of qRT-PCR analysis showed that PvSWEET24 was significantly up-regulated following treatment with NaCl, CdCl2, and HgCl2, whereas the PvSWEET5 and PvSWEET20 genes displayed a specific negative response to CdCl2 stress. Collectively, this study provides comprehensive information for the role of SWEET gene family in common bean and lays a solid foundation to elucidate the biological function of the PvSWEET gene family, as well as provide insights into the correlation between the PvSWEET genes and responses to metal stresses. [ABSTRACT FROM AUTHOR]

Sexual dimorphism in poultry, especially in Muscovy ducks, is a proven phenomenon characterized by significant differences in body weight, growth patterns, and gene expression between male and female individuals. However, there is a dearth of research on the candidate genes and mechanisms underlying these weight differences. We selected 301 Muscovy ducks and recorded their weekly body weights from birth. We utilized 3 non-linear growth models (Logistic, Bertalanffy, and Gompertz) to fit the growth curve of Muscovy ducks, it was found that the logistic model was the most suitable model for describing the growth curve of Muscovy ducks. The results from the logistic model showed that the inflection point of male Muscovy ducks occurred at a later age, and they had a heavier mature body weight than female Muscovy ducks. At 10 wk of age, we collected Muscovy duck breast muscle tissues for transcriptome sequencing (RNA-seq). To exclude the impact of weight difference, 185 differentially expressed genes (DEGs), such as PPAR, FABP3, PLIN1 , and FOXO1 , were screened. These DEGs were predominantly enriched in terms related to mitochondria, lipids, and nucleic acids. In addition, the gut microbiota has the ability to influence host physiology through the regulation of multiple processes, including playing a crucial role in host muscle growth and development. We randomly selected male and female Muscovy ducks for 16S rRNA sequencing analysis of their cecal microbiota. The results showed that there were significant differences in the composition of cecal microbiota between male and female Muscovy ducks. At the genus level, the relative abundance of Enterenecus and CAG_269 were lower in males compared to females, while Lawsonibacter, Parabacteroides_B, Streptococcus, UBA2658, Caccousia , and Butyricimonas were higher in males than in females. In summary, this study provides a scientific theoretical basis for revealing the different growth patterns of male and female Muscovy ducks, and offers explanations from both the molecular level and microbiological perspectives. [ABSTRACT FROM AUTHOR]

Cell cycle regulation plays a critical role in plant growth and development. In this study, the role of a tomato cell cycle gene SlCycB1 has been characterized. Expression analysis revealed that SlCycB1 was mostly expressed in stem, root, and leaves, with relative lower expression in flower and fruit. Tomato plants overexpressing SlCycB1 exhibited a reduction in cell number and increased cell size leading to the growth retardation. Furthermore, yeast two-hybrid analysis and bimolecular fluorescence complementation revealed that SlCycB1 interacted with histone H3.2, an essential component of the nucleosome. Histone H3.2 was transcriptionally up-regulated in the SlCycB1 overexpressing tomato lines. Furthermore, the overexpression of histone H3.2 in transgenic plants showed similar phenotypes to SlCycB1 overexpressing lines. Based on these findings, we concluded that SlCycB1 overexpression altered tomato architecture in association with histone H3.2. [ABSTRACT FROM AUTHOR]

Brassinosteroid (BR) signaling leads to the nuclear accumulation of the BRASSINAZOLE-RESISTANT 1 (BZR1) transcription factor, which plays dual roles in activating or repressing the expression of thousands of genes. BZR1 represses gene expression by recruiting histone deacetylases, but how it activates transcription of BR-induced genes remains unclear. Here, we show that BR reshapes the genome-wide chromatin accessibility landscape, increasing the accessibility of BR-induced genes and reducing the accessibility of BR-repressed genes in Arabidopsis. BZR1 physically interacts with the BRAHMA-associated SWI/SNF (BAS)-chromatin-remodeling complex on the genome and selectively recruits the BAS complex to BR-activated genes. Depletion of BAS abrogates the capacities of BZR1 to increase chromatin accessibility, activate gene expression, and promote cell elongation without affecting BZR1's ability to reduce chromatin accessibility and expression of BR-repressed genes. Together, these data identify that BZR1 recruits the BAS complex to open chromatin and to mediate BR-induced transcriptional activation of growth-promoting genes. [Display omitted] • Brassinosteroid has dual roles in reshaping the chromatin accessibility landscape • BZR1 physically interacts with the BAS complex • The BAS complex determines BR-induced transcriptional activation • BZR1 recruits the BAS complex for chromatin opening and BR-mediated skotomorphogenesis The mechanism that dictates the transcriptional activation ability of the brassinosteroid (BR) hormone remains largely unclear. Zhu et al. find that the BAS-chromatin-remodeling subcomplexes are major determinants of the transcriptional activation activity of the BR signaling pathway for allowing plants to shape their growth and development trajectory. [ABSTRACT FROM AUTHOR]

MicroRNAs are essential regulators of gene expression and have been extensively studied in plants and animals; however, few reports have been published in mushrooms. Po-MilR-1 is a novel microRNA with a length of 22 bp in Pleurotus ostreatus. The secondary structures of five precursors and the target genes of Po-MilR-1 were predicted. Expression profile analysis showed Po-MilR-1 had specific expression in the primordium and fruiting body. To explore its physiological function, Po-MilR-1 was overexpressed in P. ostreatus. The transformants showed slow mycelium growth rate and abnormal pileus with irregular edge, which suggested Po-MilR-1 plays an important role in P. ostreatus development. Additionally, Po-MilR-1 and one of its target hydrophobin genes POH1 had opposite temporal expression profiles in the primordium and fruiting body, which revealed that Po-MilR-1 may perform its physiological function through the negative regulation of POH1. This study explored the development-related function of a mushroom microRNA and will provide a reference for other microRNAs. [ABSTRACT FROM AUTHOR]

The meat production of broilers is crucial to economic benefits of broiler industries, while the slaughter performance of broilers is directly determined by skeletal muscle development. Hence, the broiler breeding for growth traits shows a great importance. As a kind of small noncoding RNA, microRNA (miRNA) can regulate the expression of multiple genes and perform a wide range of regulation in organisms. Currently, more and more studies have confirmed that miRNAs are closely associated with skeletal muscle development of chickens. Based on our previous miR-seq analysis (accession number: PRJNA668199), miR-460b-5p was screened as one of the key miRNAs probably involved in the growth regulation of chickens. However, the regulatory effect of miR-460b-5p on the development of chicken skeletal muscles is still unclear. Therefore, miR-460b-5p was further used for functional validation at the cellular level in this study. The expression pattern of miR-460b-5p was investigated in proliferation and differentiation stages of chicken primary myoblasts. It was showed that the expression level of miR-460b-5p gradually decreased from the proliferation stage (GM 50%) to the lowest at 24 h of differentiation. As differentiation proceeded, miR-460b-5p expression increased significantly, reaching the highest and stabilizing at 72 h and 96 h of differentiation. Through mRNA quantitative analysis of proliferation marker genes, CCK-8 and Edu assays, miR-460b-5p was found to significantly facilitate the transition of myoblasts from G1 to S phase and promote chicken myoblast proliferation. mRNA and protein quantitative analysis of differentiation marker genes, as well as the indirect immunofluorescence results of myotubes, revealed that miR-460b-5p significantly stimulated myotube development and promote chicken myoblast differentiation. In addition, the target relationship was validated for miR-460b-5p according to the dual-luciferase reporter assay and mRNA quantitative analysis, which indicates that miR-460b-5p was able to regulate RBM19 expression by specifically binding to the 3′ UTR of RBM19. In summary, miR-460b-5p has positive regulatory effects on the proliferation and differentiation of chicken myoblasts, and RBM19 is a target gene of miR-460b-5p. [ABSTRACT FROM AUTHOR]

Chinese cabbage is an important vegetable in Asia, and high-yielding hybrids are needed to cope with the growing demand. A comparative transcriptome profiling was conducted to reveal the differentially expressed genes (DEGs) associated with heterosis in two hybrids relative to their parents. Our data suggests that heterosis is underlined by a significant upregulation of gene expression. High expression of DEGs in glycolysis and photosynthesis pathways in hybrids depicted their relation with growth and hybrid vigor. Besides, DEGs related to auxin, abscisic acid, ethylene and gibberellin were identified, implying that these hormones may boost the mechanisms of growth and developmental processes in the hybrids. Furthermore, transcription factors, including bHLH, ERF, MYB and WRKY were predicted to regulate downstream genes linked to hybrid vigor. Collectively, the present study will be helpful for a better understanding of the regulation mechanisms of heterosis to aid cabbage yield improvement. • Transcriptional mechanisms of heterosis in Chinese cabbage was studied. • Heterosis is underlined by a significant upregulation of gene expression. • Heterosis is mainly associated with non-additive expression. • Glycolysis and photosynthesis pathways were altered in hybrids. • Phytohormones related genes play crucial role in heterosis. [ABSTRACT FROM AUTHOR]

This study was conducted in two steps to determine the effects of in ovo injection of zinc acetate (ZAC) on some gene expression associated with embryonic growth and development, and with growth and carcass characteristics of the resultant chicks. In the first step the effect of in ovo injection of ZAC on the expression of insulin-like growth factors (IGFs:IGF-I and IGF-I), myogenic regulatory factors (MRFs) and metallothionein (MT) genes was examined, and in the step two, the associations between genes expression with fertility, embryonic mortality, hatchability, body weight (BW) and relative organ weight on day of hatch, and body weight (BW) and feed conversion ratio (FCR) a week after hatching were investigated. Seven hundred twenty fertile eggs (n=720) were randomly divided into 4 treatment groups consisted of: 1) noninjected (NI) group, 2) sham group (group injected with deionized water (DW)), and 3) and 4) groups injected with 3.64 and 5.23 M ZAC, respectively. On day 3 of incubation the eggs were injected with 50 µL of each treatment into the albumen. On day 5 of the incubation and on hatch day, liver and breast muscle of the chicks were removed and immediately stored at -80 °C until RNA extraction and real time-PCR analysis. In ovo ZAC injection increased myogenic differentiation factor both in embryo and breast muscle. MT mRNA expression was also increased by ZAC injection. Hatchability was lower in ZAC groups and early embryonic mortality was higher in sham control (SHC) and ZAC groups. Injection of ZAC improved both BW and FCR during the first week of rearing, and increased the relative weights of liver and breast muscle. In conclusion, in ovo injection of ZAC increased some of gene expressions of tissues and BW7 during the first week, but decreased hatchability. Hence, lower doses of ZAC are recommended to use in further experiments. [ABSTRACT FROM AUTHOR]

Antidepressants are among the most commonly detected pharmaceuticals in aqueous systems, and, as emerging organic pollutants, may exert negative effects on non-target aquatic organisms. Previously, it has been revealed that antidepressant exposure significantly inhibits the growth and development of fish during their early developmental stages. Thus, in the present study, we aimed to identify and compare the underlying mechanisms of action of different antidepressants at the transcriptional level using zebrafish ( Danio rerio ) embryos. Through high-throughput RNA sequencing (RNA-Seq) data analysis, 32, 34, and 130 differentially expressed genes (DEGs) were obtained from zebrafish larvae after 120 h of embryonic exposure to sublethal concentrations of amitriptyline, fluoxetine, and mianserin, respectively. The expression profiles of the identified DEGs showed similar trends in response to the three antidepressant treatments, suggesting consistent toxic effects of low concentrations of these three drugs on the regulation of gene expression in fish. Several metabolic and signaling pathways, including glycolysis/gluconeogenesis and the insulin pathway, were affected in the exposed fish larvae. The expression profiles of selected DEGs were then verified by the qRT-PCR method, which indicated significant positive correlations with the RNA-Seq results. Next, we determined the concentration-dependent expression patterns of 6 selected DEGs in fish larvae exposed to three antidepressants at a series of environmentally relevant concentrations. The results revealed a significant concentration-dependent reduction in the levels of dual-specificity phosphatase 5 ( dusp5 ) mRNA, as well as a non-concentration-dependent gene expression inhibition of prostaglandin D2 synthase b ( ptgdsb ); the circadian rhythm-related genes, i.e. those encoding nuclear receptor subfamily 1, group D, member 1 ( nr1d1 ) and period 2 ( per2 ); and genes encoding early growth response factors ( egr1 and egr4 ), in the antidepressant-treated fish larvae. In summary, to our knowledge, our findings demonstrate, for the first time, that the three different categories of antidepressants have common effects on the gene expression involved in multiple biological processes and signaling pathways during the early development of fish and thus provide information for characterizing the adverse outcome pathways and on the ecological risk assessment of these pharmaceutical pollutants in the aquatic environment. [ABSTRACT FROM AUTHOR]

Fruit set and early development depends on endogenous hormone levels and gene expression related to fruit growth and development in cucumber (Cucumis sativus). In this study, the growth and development of cucumber ovaries and young fruits, endogenous hormones levels, and Csexpansin 10 (CsEXP 10) gene expressions in pollinated fruits and unpollinated ovaries were studied from -2 to 6 days post anthesis (DPA). The results showed that the fruit diameter and length, single fruit weight, endogenous hormone levels, and CsEXP 10 gene expression levels were all higher in pollinated fruits than in unpollinated ovaries, and CsEXP 10 gene expression levels were positively correlated with indole-3-acetic acid (IAA), but negatively correlated with gibberellic acid (GA3) and abscisic acid (ABA). This suggests that pollination may stimulate the fruit set and development by inducing increases in endogenous hormone levels and CsEXP 10 gene expression, and the CsEXP 10 gene may be downregulated by GA3 and ABA., and. [ABSTRACT FROM AUTHOR]

Using melatonin as a gestational therapeutic due to its antioxidant and vasodilative properties increases fetal morphometric measurements in ruminant models, however its effects on gestating swine and fetal circadian regulation remain unknown. This study evaluated the effects of dietary melatonin supplementation during gestation on fetal hepatic circadian regulatory and metabolic gene expression. Twenty-four pregnant sows were randomly assigned to either melatonin (20mg/d; MEL) or control (CON) and 0500h (AM) or 1700h (PM) harvest timepoint across fall and spring replicates. The fall replicate occurred from gestational day 38±1 to 99±1, while spring was days 41 to 106±1. At harvest small, medium, and large piglets were identified by body weight and their livers were collected. Data were analyzed using a linear mixed model by the MIXED procedure of SAS. Cry1 expression tended to increase (P=0.0575) in large fetuses compared to small during the fall, while large fetuses had the greatest expression, medium intermediary, and small least during the spring (P=0.0056). Cry2 was reduced (P< 0.001) in MEL offspring compared to CON in the fall. There was a Treatment × Class interaction (P=0.0104) for Cry2 expression during spring wherein, CON-AM was reduced compared to CON-PM, however no differences between MEL groups. A Treatment × Class interaction (P=0.0511) of Per2 expression was present in the fall, where expression of small control fetuses was reduced compared to remaining controls. Spring Per2 expression increased (P=0.0122) in large fetuses compared to other sizes, Per2 also increased (P=0.0039) in PM compared to AM. Fall IGF1 expression increased (P=0.0366) in large fetuses compared to medium and small, and spring IGF1 expression increased (P=0.0067) in large fetuses compared to small. These findings suggest that maternal melatonin supplementation during gestation modulates expression of hepatic circadian regulatory and metabolic genes which may impact growth and developmental efficiency postnatally in a seasonal manner. [ABSTRACT FROM AUTHOR]

The NITRATE TRANSPORTER 1/PEPTIDE TRANSPORTER FAMILY (NPF) genes, initially characterized as nitrate or peptide transporters in plants, are involved in the transport of a large variety of substrates, including amino acids, nitrate, auxin (IAA), jasmonates (JAs), abscisic acid (ABA) and gibberellins (GAs) and glucosinolates. A total of 169 potential functional NPF genes were excavated in Brassica napus, and they showed diversified expression patterns in 90 different organs or tissues based on transcriptome profile data. The complex time-serial expression changes were found for most functional NPF genes in the development process of leaves, silique walls and seeds, which indicated that the expression of Brassica napus NPF (BnaNPF) genes may respond to altered phytohormone and secondary metabolite content through combining with promoter element enrichment analysis. Furthermore, many BnaNPF genes were detected to respond to vernalization with two different patterns, and 20 BnaNPF genes responded to nitrate deficiency. These results will provide useful information for further investigation of the biological function of BnaNPF genes for growth and development in rapeseed. [ABSTRACT FROM AUTHOR]