Regional Active Transcription Associates with Homoeologous Exchange Breakpoints in Synthetic Brassica Tetraploids.

Polyploidization plays a crucial role in plant evolution and is becoming increasingly important in breeding. Structural variations and epigenomic repatterning have been observed in synthetic polyploidizations. However, the mechanisms underlying the occurrence and their effects on gene expression and phenotype remain unknown. Here, we investigated genome-wide large deletion/duplication regions (DelDups) and genomic methylation dynamics in leaf organs of progeny from the first eight generations of synthetic tetraploids derived from Chinese cabbage (Brassica rapa L. ssp. pekinensis) and cabbage (Brassica oleracea L. var. capitata). One- or two-copy DelDups, with a mean size of 5.70 Mb (400 kb - 65.85 Mb), occurred from the first generation of selfing and thereafter. The duplication of a fragment in one subgenome consistently coincided with the deletion of its syntenic fragment in the other subgenome, and vice versa, indicating that these DelDups were generated by homoeologous exchanges (HEs). Interestingly, the larger the genomic syntenic region, the higher the frequency of DelDups, further suggesting that the pairing of large homoeologous fragments is crucial for HEs. Moreover, we found that the active transcription of continuously distributed genes in local regions is positively associated with the occurrence of HE breakpoints. In addition, the expression of genes within DelDups exhibited a dosage effect, and plants with extra parental genomic fragments generally displayed phenotypes biased towards the corresponding parent. Genome-wide methylation fluctuated remarkably, which did not clearly affect gene expression on a large scale. Our findings provide insights into the early evolution of polyploid genomes, offering valuable knowledge for polyploidization-based breeding.

Enhancing cold resistance in Banana (Musa spp.) through EMS-induced mutagenesis, L-Hyp pressure selection: phenotypic alterations, biomass composition, and transcriptomic insights.

BACKGROUND: The cultivation of bananas encounters substantial obstacles, particularly due to the detrimental effects of cold stress on their growth and productivity. A potential remedy that has gained attention is the utilization of ethyl mesylate (EMS)-induced mutagenesis technology, which enables the creation of a genetically varied group of banana mutants. This complex procedure entails subjecting the mutants to further stress screening utilizing L-Hyp in order to identify those exhibiting improved resistance to cold. This study conducted a comprehensive optimization of the screening conditions for EMS mutagenesis and L-Hyp, resulting in the identification of the mutant cm784, which exhibited remarkable cold resistance. Subsequent investigations further elucidated the physiological and transcriptomic responses of cm784 to low-temperature stress. RESULTS: EMS mutagenesis had a substantial effect on banana seedlings, resulting in modifications in shoot and root traits, wherein a majority of seedlings exhibited delayed differentiation and limited elongation. Notably, mutant leaves displayed altered biomass composition, with starch content exhibiting the most pronounced variation. The application of L-Hyp pressure selection aided in the identification of cold-resistant mutants among seedling-lethal phenotypes. The mutant cm784 demonstrated enhanced cold resistance, as evidenced by improved survival rates and reduced symptoms of chilling injury. Physiological analyses demonstrated heightened activities of antioxidant enzymes and increased proline production in cm784 when subjected to cold stress. Transcriptome analysis unveiled 946 genes that were differentially expressed in cm784, with a notable enrichment in categories related to 'Carbohydrate transport and metabolism' and 'Secondary metabolites biosynthesis, transport, and catabolism'. CONCLUSION: The present findings provide insights into the molecular mechanisms that contribute to the heightened cold resistance observed in banana mutants. These mechanisms encompass enhanced carbohydrate metabolism and secondary metabolite biosynthesis, thereby emphasizing the adaptive strategies employed to mitigate the detrimental effects induced by cold stress.

Phenotypic variations induced emergence of orientation order and morphology in Bacillus subtilis biofilm growth.

During the Bacillus subtilis biofilm growth on the solid MSgg substrate, the biofilm exhibits highly ordered structures such as matrix-producing-cell chains and Van Gogh bundles due to bacterial orientation order. These structures make the biofilm have strong mobility and environmental adaptability, thus making bacteria easier to survive and thrive in biofilms comparing to planktonic bacteria. We tested the behaviors of different phenotypes as well as their impacts on bacterial clusters: motile cells arrange disorderly, the biofilm made up of motile cells tends to be circular and isotropic; matrix-producing cells form cellular chains that guide motile cells along the chain to form a locally nematic phase, the morphology of the biofilm made up of both motile cells and matrix-producing cells is rendered irregular. Combining the results of a coarse-grained and individual-based model, we can control the biofilm growth through regulating environmental friction, bacterial growth rate and adhesion between cells.

Mechanisms and biological impacts of graphene and multi-walled carbon nanotubes on Drosophila melanogaster: Oxidative stress, genotoxic damage, phenotypic variations, locomotor behavior, parasitoid resistance, and cellular immune response.

The use of graphene and multi-walled carbon nanotubes (MWCNTs) has now become rather common in medical applications as well as several other areas thanks to their useful physicochemical properties. While in vitro testing offers some potential, in vivo research into toxic effects of graphene and MWCNTs could yield much more reliable data. Drosophila melanogaster has recently gained significant popularity as a dynamic eukaryotic model in examining toxicity, genotoxicity, and biological effects of exposure to nanomaterials, including oxidative stress, cellular immune response against two strains (NSRef and G486) of parasitoid wasp (Leptopilina boulardi), phenotypic variations, and locomotor behavior risks. D. melanogaster was used as a model organism in our study to identify the potential risks of exposure to graphene (thickness: 2-18 nm) and MWCNTs in different properties (as pure [OD: 10-20 nm short], modified by amide [NH2 ] [OD: 7-13 nm length: 55 µm], and modified by carboxyl [COOH] [OD: 30-50 nm and length: 0.5-2 µm]) at concentrations ranging from 0.1 to 250 µg/ml. Significant effects were observed at two high doses (100 and 250 µg/ml) of graphene or MWCNTs. This is the first study to report findings of cellular immune response against hematopoiesis and parasitoids, nanogenotoxicity, phenotypic variations, and locomotor behavior in D. melanogaster.

Hazard Assessment of the Effects of Acute and Chronic Exposure to Permethrin, Copper Hydroxide, Acephate, and Validamycin Nanopesticides on the Physiology of Drosophila: Novel Insights into the Cellular Internalization and Biological Effects.

New insights into the interactions between nanopesticides and edible plants are required in order to elucidate their impacts on human health and agriculture. Nanopesticides include formulations consisting of organic/inorganic nanoparticles. Drosophila melanogaster has become a powerful model in genetic research thanks to its genetic similarity to mammals. This project mainly aimed to generate new evidence for the toxic/genotoxic properties of different nanopesticides (a nanoemulsion (permethrin nanopesticides, 20 ± 5 nm), an inorganic nanoparticle as an active ingredient (copper(II) hydroxide [Cu(OH)2] nanopesticides, 15 ± 6 nm), a polymer-based nanopesticide (acephate nanopesticides, 55 ± 25 nm), and an inorganic nanoparticle associated with an organic active ingredient (validamycin nanopesticides, 1177 ± 220 nm)) and their microparticulate forms (i.e., permethrin, copper(II) sulfate pentahydrate (CuSO4·5H2O), acephate, and validamycin) widely used against agricultural pests, while also showing the merits of using Drosophila-a non-target in vivo eukaryotic model organism-in nanogenotoxicology studies. Significant biological effects were noted at the highest doses of permethrin (0.06 and 0.1 mM), permethrin nanopesticides (1 and 2.5 mM), CuSO4·5H2O (1 and 5 mM), acephate and acephate nanopesticides (1 and 5 mM, respectively), and validamycin and validamycin nanopesticides (1 and 2.5 mM, respectively). The results demonstrating the toxic/genotoxic potential of these nanopesticides through their impact on cellular internalization and gene expression represent significant contributions to future nanogenotoxicology studies.

Genome-wide association study identifies various loci underlying agronomic and morphological traits in diversified potato panel.

Potato is one of the most important food crops all over the world. Breeding activities for this crop are mainly aimed to improve the quality and yield of tuber. However, genetic architecture of various traits contributing to the quality and yield of potato are not yet completely understood. Genome wide association studies provides a broader way to identify the genomic regions associated with various traits. Panels of 237 tetraploid potato genotypes from different countries were grown for two consecutive years 2016 and 2017 at experimental research area of Potato research center Nigde, Turkey. A genome wide association study using SolCAP 12K array was performed for various morpho-agronomic traits. Structure algorithm and neighborhood joining analysis clearly divided all genotypes into 4 clusters on the basis of their origin. For the marker trait association, Mixed Linear Model in TASSEL was performed and 36 genomic regions were found for the traits under study. The mean r2 value was found to be 0.92 and mean significant LD was 47.5% in the populations. LD patterns reflected the breeding history of potato. The findings of present study provide a framework which could be useful for future potato breeding programs to enhance the production and to reduce the challenges in the coming years to feed world's population.

Sub-species diversity of Xanthomonas euvesicatoria Bulgarian and Macedonian strains from pepper.

Sub-species diversity of pepper populations of Xanthomonas euvesicatoria in Bulgaria and Macedonia in 2012 was the object of this study. Species determination of 44 strains was performed by molecular methods using two pairs of species-specific primers and RFLP (restriction fragment length polymorphism) analysis of the 16S-23S ITS region with HpaII. The populations were characterized by genotypic and phenotypic properties. The genotypic diversity of the strains was evaluated by RAPD (random amplified polymorphic DNA) technique. Primer CUGEA-6 differentiated the strains in two groups, one of which included only Bulgarian strains and revealed a mixed profile of the type strain. BiologTM metabolite profiles separated the strains in four groups: two of which were composed only of Bulgarian or Macedonian strains. Correlation between the RAPD and the metabolic profiles was observed. Twelve antibiotics and copper ions in five concentrations (1-5 g kg-1) were tested for biological activity. The inhibition zones of the Bulgarian strains were statistically proven to be considerably larger than the Macedonian ones in the tests with kanamycin, streptomycin, polymyxin B sulphate, tetracycline and vankomycin. The inhibition zones of the Bulgarian strains were statistically proven to be relatively larger than the Macedonian ones in the copper tests. Based on our studies the Macedonian population of X. euvesicatoria manifested a relative homogeneity while a greater diversity was observed in the Bulgarian population.

Phenotypic variation in hypocotyl elongation among elite sand rice (Agriophyllum squarrosum) lines.

Sand rice (Agriophyllum squarrosum), widely distributed in Central Arid Asia and prevalent in the sand dunes of northern China, presents a promising potential as a climate-resilient crop. The plasticity of hypocotyl growth is the key trait for sand rice to cope with wind erosion and sand burial, ensure seedling emergence, and determine plant architecture. In this study, we assessed the overall hypocotyl phenotype of six sand rice elite lines, which were collected from different regions of northern China, and selected by our group over past decade through common garden trials. Significant phenotypic variations were observed in thousand-seed weight (TSW), seedling emergence percentage, hypocotyl length and diameter, and seedling fresh weight among the lines. The elite line Aerxiang (AEX) exhibited excellent agronomic performance with superior and synchronous emergence, and high survival percentage, distinguishing itself as a prime candidate for further large-scale cultivation. Contrastingly, the lines from the arid regions showed markedly lower performance. Partial Least Squares Path Modeling (PLSPM) was used to assess the impact of seed provenance climate factors, including annual mean temperature (AMT) and annual mean precipitation (AMP), on trait variability among lines. The findings indicate a significant correlation between climate factors and hypocotyl length, highlighting the intricate adaptation of sand rice to local climate. The comprehensive understanding of the mechanisms behind phenotypic variations offers valuable insights for sand rice de novo domestication and innovative germplasm resources, and lays the foundation for ecological restoration in sandy areas.

Is intraspecific trait differentiation in Parthenium hysterophorus a consequence of hereditary factors and/or phenotypic plasticity?

Of the various strategies adopted by an invasive plant species for expanding its niche breadth, phenotypic differentiation (either due to plasticity and/or adaptive evolution) is proven to be the most successful. Lately, we studied the persistence of substantial morpho-functional variations within the individuals of alien invasive plant, Parthenium hysterophorus in Chandigarh, India, through field surveys. Based on observed differences, the individuals were categorized into two morphotypes, PA and PB. PA had higher leaf area, leaf biomass, and chlorophyll content as compared with PB. However, PB had a higher stem circumference, stem specific density, twig dry matter content, profuse branching, bigger canopy, and better reproductive output than PA. To substantiate the persistence of intraspecific variations in P. hysterophorus and to deduce the possible genesis of these variations, we propagated both the morphotypes under experimental conditions in winter and summer. Apart from the key morpho-functional differences observed during the field studies, protein and carbohydrate metabolism were studied in leaves and roots of the propagated plants. Differences in plant metabolism were observed only during the early growth period, whereas the morpho-functional traits varied in the mature flowering plants. The effect of growth season was highly significant on all the studied morpho-functional and biochemical parameters (p ≤ 0.05). Parent morphotypes (P) and interactions between morphotypes and seasons significantly affected several growth parameters (p ≤ 0.05). The analyses revealed that the contrasting growth conditions at the time of transplantation and early growth may regulate the phenotype of P. hysterophorus. The pattern of intraspecific variations observed during the study is justified to consider morphotype PA as winter biotype and morphotype PB as summer biotype of P. hysterophorus. The study points towards the role of plasticity or a combination of genetic and environmental (G × E) factors in producing the phenotypic variability observed in the population of P. hysterophorus.

Phenotypic variations in ocular features among siblings with oculocutaneous albinism.

Purpose: To assess the clinical profiles, presenting ocular features, and variations in the phenotypic features in siblings with oculocutaneous albinism (OCA). Methods: Electronic medical records of consecutive siblings diagnosed with albinism from January 2016 to December 2020 were reviewed to identify the affected siblings. The variations in their phenotypic characteristics were studied. Results: Significant variations were observed in the clinical features between the siblings (n = 42). A difference of >2 lines in visual acuity was observed in 50% (n = 21) of the sibling pairs. Compound hyperopic astigmatism was the commonest refractive error. The refractive status was different in 80.95% (n = 34) pairs. Although individually strabismus and abnormal head posture were observed in one-third and one-fourth of individual children, respectively, both siblings with similar strabismus were seen in only 16.67% (n = 7) and with a similar abnormal head posture in 13.33% (n = 5). Nystagmus was the most consistent finding across these siblings with a similar nature of horizontal jerk or pendular in 65% of sibling pairs. Conclusion: This study observed significant variations in phenotypic presentations among siblings with OCA. Such differences in clinical manifestations and severity would be helpful in appropriate counseling of these families as the need for rehabilitation services is likely to vary across siblings.

Expanding the phenotypic spectrum of KCNK4: From syndromic neurodevelopmental disorder to rolandic epilepsy.

The KCNK4 gene, predominantly distributed in neurons, plays an essential role in controlling the resting membrane potential and regulating cellular excitability. Previously, only two variants were identified to be associated with human disease, facial dysmorphism, hypertrichosis, epilepsy, intellectual/developmental delay, and gingival overgrowth (FHEIG) syndrome. In this study, we performed trio-based whole exon sequencing (WES) in a cohort of patients with epilepsy. Two de novo likely pathogenic variants were identified in two unrelated cases with heterogeneous phenotypes, including one with Rolandic epilepsy and one with the FHEIG syndrome. The two variants were predicted to be damaged by the majority of in silico algorithms. These variants showed no allele frequencies in controls and presented statistically higher frequencies in the case cohort than that in controls. The FHEIG syndrome-related variants were all located in the region with vital functions in stabilizing the conductive conformation, while the Rolandic epilepsy-related variant was distributed in the area with less impact on the conductive conformation. This study expanded the genetic and phenotypic spectrum of KCNK4. Phenotypic variations of KCNK4 are potentially associated with the molecular sub-regional effects. Carbamazepine/oxcarbazepine and valproate may be effective antiepileptic drugs for patients with KCNK4 variants.

The magnitude of heterogeneity in individual-cell growth dynamics is an inherent characteristic of Salmonella enterica ser. Typhimurium strains.

Individual-cell heterogeneity is a major source of variability in biological systems affecting importantly, among others, microbial behavior. Characterization of cell populations of pathogenic bacterial strains in their entirety, ignoring the phenotypic variability of single cells, may result in erroneous safety risk estimates. The objective of the present study was the evaluation and comparison of the heterogeneity in the individual-cell growth dynamics of different strains of Salmonella enterica. The stochasticity in the growth of single cells of five S. enterica ser. Typhimurium strains was quantitatively described using time-lapse microscopy, and the existence of a strain effect was statistically assessed. In total, 831 growing microcolonies originating from single cells were monitored and analyzed, and the growth kinetic parameters of lag time (λ) and maximum specific growth rate (µmax) for each one of them were estimated. An extensive heterogeneity in individual-cell growth kinetics was recorded, while significant inter-strain differences in their heterogeneity were evident based on simultaneous Bonferroni confidence intervals and Levene's tests. The Logistic and LogLogistic probability distribution provided the best fitting for µmax and λ data, respectively for all the tested strains. The strain effect on the above distributions was also demonstrated with pairwise comparisons of the decile differences. The impact of strain-dependent heterogeneity on microbial growth was visualized by comparing stochastic growth curves of different strains using Monte Carlo simulation. In conclusion, the individual-cell growth dynamics of S. enterica are heterogeneous, with the magnitude of the observed heterogeneity appearing to be an inherent characteristic of bacterial strains.

Rapid-onset dystonia-parkinsonism with ATP1A3 mutation and left lower limb paroxysmal dystonia.

BACKGROUND: Rapid-onset dystonia-parkinsonism (RDP) is a disease characterized by an abrupt onset of dystonia accompanied by signs of parkinsonism and prominent bulbar symptoms. CASE REPORT: We describe a case of a female patient, born after normal delivery, but diagnosed with mild intellectual disability at age 7. She presented with an abrupt onset of upper limb dystonia and bradykinesia without tremor in parkinsonism, as well as dysarthria and dysphagia caused by prominent bulbar symptoms, at age 9. She had normal findings on brain magnetic resonance imaging, electroencephalography, and blood examination but was diagnosed with a psychogenic disorder. At age 10, she developed left lower limb paroxysmal stiffness with pain, and at 14, she was hospitalized due to lasting paroxysmal symptoms. Whole-exome sequencing was performed for this index case and her parents, and a de novo missense variant c.829G > A, p.Glu277Lys in ATP1A3 was identified. DISCUSSION: This RDP case highlights a rare clinical feature of paroxysmal dystonia that affects the lower left limb and develops after the abrupt onset of permanent dystonia. Currently, there are only three reported RDP cases associated with the same missense mutation, and we summarized the clinical features of all cases including ours, such as onset of age, time for stable, RDP score, relapse and exacerbation. Various symptoms owing to ATP1A3 mutation could develop as ATP1A3-related neurological disorders beyond classical phenotypes such as alternating hemiplegia of childhood (AHC) or RDP. Although RDP is extremely rare during childhood, it is important to understand its clinical characteristics in children.

Evaluation of the Prevalence, Regional Phenotypic Variation, Comorbidities, Risk Factors, and Variations in Response to Different Therapeutic Modalities Among Indian Women: Proposal for the Indian Council of Medical Research-Polycystic Ovary Syndrome (ICMR-PCOS) Study.

BACKGROUND: There is scanty data in India on polycystic ovary syndrome (PCOS) from several small, undersized, convenience-based studies employing differing diagnostic criteria and reporting varied regional prevalence. It is difficult to draw clear-cut conclusions from these studies; therefore, the present multicentric, well-designed, large-scale representative countrywide epidemiological study on PCOS across India was conceived with the aim to generate the actual prevalence rates of PCOS in India with a total sample size of approximately 9000 individuals. OBJECTIVE: The primary objectives of the study are to estimate the national prevalence of PCOS in India and the burden of comorbidities and to compare the variation in efficacy of standard therapeutic modalities for metabolic dysfunction in women with PCOS. METHODS: This multicentric umbrella study consists of three different substudies. Substudy 1 will involve recruitment of women aged 18-40 years using a multistage sampling technique from randomly selected polling booths across urban and rural areas to estimate national prevalence, phenotypic variation, and risk factors among regions. Substudy 2 involves recruitment of subjects from the community pool of substudy 1 and the institutional pool for quantitation of comorbidities among women with PCOS. Substudy 3, an interventional part of the study, aims for comparison of variation in efficacies of common treatment modalities and will be conducted only at 2 centers. The eligible consenting women will be randomized in a 1:1 ratio into 2 arms through a blinding procedure. All these women will undergo clinical, biochemical, and hormonal assessment at baseline and at 3 and 6 months. The data generated will be analyzed using the reliable statistical software SPSS (version 26). RESULTS: The study is ongoing and is likely to be completed by April 2022. The data will be compiled and analyzed, and the results of the study will be disseminated through publications. CONCLUSIONS: The Indian Council of Medical Research-PCOS study is the first of its kind attempting to provide accurate and comprehensive data on prevalence of PCOS in India. TRIAL REGISTRATION: Clinical Trials Registry-India CTRI/2018/11/016252; ctri.nic.in/Clinicaltrials/pmaindet2.php?trialid=26366. INTERNATIONAL REGISTERED REPORT IDENTIFIER (IRRID): DERR1-10.2196/23437.

Replicative Aging in Pathogenic Fungi.

Candida albicans, Candida auris, Candida glabrata, and Cryptococcus neoformans are pathogenic yeasts which can cause systemic infections in immune-compromised as well as immune-competent individuals. These yeasts undergo replicative aging analogous to a process first described in the nonpathogenic yeast Saccharomyces cerevisiae. The hallmark of replicative aging is the asymmetric cell division of mother yeast cells that leads to the production of a phenotypically distinct daughter cell. Several techniques to study aging that have been pioneered in S. cerevisiae have been adapted to study aging in other pathogenic yeasts. The studies indicate that aging is relevant for virulence in pathogenic fungi. As the mother yeast cell progressively ages, every ensuing asymmetric cell division leads to striking phenotypic changes, which results in increased antifungal and antiphagocytic resistance. This review summarizes the various techniques that are used to study replicative aging in pathogenic fungi along with their limitations. Additionally, the review summarizes some key phenotypic variations that have been identified and are associated with changes in virulence or resistance and thus promote persistence of older cells.

Phenotypic Trait Variation as a Response to Altitude-Related Constraints in Arabidopsis Populations.

Natural variations help in identifying genetic mechanisms of morphologically and developmentally complex traits. Mountainous habitats provide an altitudinal gradient where one species encounters different abiotic conditions. We report the study of 341 individuals of Arabidopsis thaliana derived from 30 natural populations not belonging to the 1001 genomes, collected at increasing altitudes, between 200 and 1800 m in the Pyrenees. Class III peroxidases and ribosomal RNA sequences were used as markers to determine the putative genetic relationships among these populations along their altitudinal gradient. Using Bayesian-based statistics and phylogenetic analyses, these Pyrenean populations appear with significant divergence from the other regional accessions from 1001 genome (i.e., from north Spain or south France). Individuals of these populations exhibited varying phenotypic changes, when grown at sub-optimal temperature (22 vs. 15°C). These phenotypic variations under controlled conditions reflected intraspecific morphological variations. This study could bring new information regarding the west European population structure of A. thaliana and its phenotypic variations at different temperatures. The integrative analysis combining genetic, phenotypic variation and environmental datasets is used to analyze the acclimation of population in response to temperature changes. Regarding their geographical proximity and environmental diversity, these populations represent a tool of choice for studying plant response to temperature variation. HIGHLIGHTS: -Studying the natural diversity of A. thaliana in the Pyrenees mountains helps to understand European population structure and to evaluate the phenotypic trait variation in response to climate change.

Adaptive phenotypic variation among clonal ant workers.

Phenotypic variations are observed in most organisms, but their significance is not always known. The phenotypic variations observed in social insects are exceptions. Genetically based response threshold variances have been identified among workers and are thought to play several important adaptive roles in social life, e.g. allocating tasks among workers according to demand, promoting the sustainability of the colony and forming the basis of rationality in collective decision-making. Several parthenogenetic ants produce clonal workers and new queens by asexual reproduction. It is not clearly known whether such genetically equivalent workers show phenotypic variations. Here, we demonstrate that clonal workers of the parthenogenetic ant Strumigenys membranifera show large threshold variances among clonal workers. A multi-locus genetic marker confirmed that colony members are genetic clones, but they showed variations in their sucrose response thresholds. We examined the changing pattern of the thresholds over time generating hypotheses regarding the mechanism underlying the observed phenotypic variations. The results support the hypothesis that epigenetic modifications that occur after eclosion into the adult form are the cause of the phenotypic variations in this asexual species.

Genes and Small RNA Transcripts Exhibit Dosage-Dependent Expression Pattern in Maize Copy-Number Alterations.

Copy-number alterations are widespread in animal and plant genomes, but their immediate impact on gene expression is still unclear. In animals, copy-number alterations usually exhibit dosage effects, except for sex chromosomes which tend to be dosage compensated. In plants, genes within small duplications (<100 kb) often exhibit dosage-dependent expression, whereas large duplications (>50 Mb) are more often dosage compensated. However, little or nothing is known about expression in moderately-sized (1-50 Mb) segmental duplications, and about the response of small RNAs to dosage change. Here, we compared maize (Zea mays) plants with two, three, and four doses of a 14.6-Mb segment of chromosome 1 that contains ∼300 genes. Plants containing the duplicated segment exhibit dosage-dependent effects on ear length and flowering time. Transcriptome analyses using GeneChip and RNA-sequencing methods indicate that most expressed genes and unique small RNAs within the duplicated segments exhibit dosage-dependent transcript levels. We conclude that dosage effect is the predominant regulatory response for both genes and unique small RNA transcripts in the segmental dosage series we tested. To our knowledge this is the first analysis of small RNA expression in plant gene dosage variants. Because segmental duplications comprise a significant proportion of eukaryotic genomes, these findings provide important new insight into the regulation of genes and small RNAs in response to dosage changes.