title: PeerJ description: Articles published in PeerJ link: https://peerj.com/articles/index.rss3?journal=peerj&page=787 creator: info@peerj.com PeerJ errorsTo: info@peerj.com PeerJ language: en title: 3D reconstruction identifies loci linked to variation in angle of individual sorghum leaves link: https://peerj.com/articles/12628 last-modified: 2021-12-22 description: Selection for yield at high planting density has reshaped the leaf canopy of maize, improving photosynthetic productivity in high density settings. Further optimization of canopy architecture may be possible. However, measuring leaf angles, the widely studied component trait of leaf canopy architecture, by hand is a labor and time intensive process. Here, we use multiple, calibrated, 2D images to reconstruct the 3D geometry of individual sorghum plants using a voxel carving based algorithm. Automatic skeletonization and segmentation of these 3D geometries enable quantification of the angle of each leaf for each plant. The resulting measurements are both heritable and correlated with manually collected leaf angles. This automated and scaleable reconstruction approach was employed to measure leaf-by-leaf angles for a population of 366 sorghum plants at multiple time points, resulting in 971 successful reconstructions and 3,376 leaf angle measurements from individual leaves. A genome wide association study conducted using aggregated leaf angle data identified a known large effect leaf angle gene, several previously identified leaf angle QTL from a sorghum NAM population, and novel signals. Genome wide association studies conducted separately for three individual sorghum leaves identified a number of the same signals, a previously unreported signal shared across multiple leaves, and signals near the sorghum orthologs of two maize genes known to influence leaf angle. Automated measurement of individual leaves and mapping variants associated with leaf angle reduce the barriers to engineering ideal canopy architectures in sorghum and other grain crops. creator: Michael C. Tross creator: Mathieu Gaillard creator: Mackenzie Zwiener creator: Chenyong Miao creator: Ryleigh J. Grove creator: Bosheng Li creator: Bedrich Benes creator: James C. Schnable uri: https://doi.org/10.7717/peerj.12628 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2021 Tross et al. title: Small herbivores and abiotic heterogeneity promote trait variation of a saltmarsh plant in local communities link: https://peerj.com/articles/12633 last-modified: 2021-12-22 description: Intraspecific trait variation (ITV) enables plants to respond to global changes. However, causes for ITV, especially from biotic components such as herbivory, are not well understood. We explored whether small vertebrate herbivores (hares and geese) impact ITV of a dominant clonal plant (Elytrigia atherica) in local communities. Moreover, we looked at the relative importance of their direct (e.g., selective grazing) and indirect effects (altering genotypic richness/diversity and abiotic environment) on ITV. We used exclosures at two successional stages in a Dutch saltmarsh, where grazing pressure at the early successional stage was ca. 1.5 times higher than that of the intermediate successional stage. We measured key functional traits of E. atherica including height, aboveground biomass, flowering (flower or not), specific leaf area, and leaf dry matter content in local communities (1 m × 1 m plots) inside and outside the exclosures. We determined genotypic richness and diversity of each plant using molecular markers. We further measured abiotic variations in topography and clay thickness (a proxy for soil total nitrogen). Structural equation models revealed that small herbivores significantly promoted ITV in height and flowering at the early successional stage, while they marginally promoted ITV in height at the intermediate successional stage. Moreover, the direct effects of herbivores played a major role in promoting ITV. Small herbivores decreased genotypic diversity at the intermediate successional stage, but genotypic richness and diversity did not impact ITV. Small herbivores did not alter topographic variation and variation in clay thickness, but these variations increased ITV in all traits at the early successional stage. Small herbivores may not only impact trait means in plants as studies have shown but also their ITV. creator: Qingqing Chen creator: Christian Smit creator: Ido Pen creator: Han Olff uri: https://doi.org/10.7717/peerj.12633 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2021 Chen et al. title: Ferric citrate is a safe and digestible source of iron in broilers and piglets link: https://peerj.com/articles/12636 last-modified: 2021-12-22 description: BackgroundIron (Fe) is traditionally supplemented in poultry and swine diets using inorganic forms (e.g. sulfates, oxides). However, research suggests that organic sources are more beneficial due to greater bioavailability. In this paper, we present results from four studies aimed at assessing ferric citrate (CI-FER™, Akeso Biomedical Inc., Burlington, MA, USA) as a safe and effective source of Fe for broilers and piglets.MethodsA total of four studies were performed in Germany following standard farming practices for each species. One study in day-old broiler chicks and one study in weaned piglets were designed as target animal safety studies where animals were randomly allocated to one of three treatment groups: a negative control group, the proposed dose group and a multifold dose group. Broilers and pigs were fed the experimental diets for 35 and 42 days, respectively. In each study, average daily feed intake, average daily weight gain and feed conversion ratio were measured, and blood samples were taken at study end for routine biochemistry and haematology. The other two studies were designed to evaluate different sources of dietary Fe for weaned piglets bred and managed under standard farm conditions. All piglets received routine Fe injections (200 mg Fe dextran, intramuscular) on day 3 of age, as well as the experimental diets for 42 days. In both studies, performance parameters were measured. In one study, Fe digestibility and serum Fe, superoxide dismutase and haptoglobin were also measured. In all studies, the general health status of the animals was monitored daily and all culls and mortality recorded. Each study followed a complete randomised block design.ResultsIn broilers, ferric citrate was well tolerated up to 2,000 mg/kg feed (×10 the recommended inclusion rate) and no adverse effects on growth, blood parameters or mortality were observed. In piglets, ferric citrate was well tolerated up to 5,000 mg/kg feed (×10 the recommended inclusion rate) with no adverse effects on growth, blood parameters or mortality. In addition, piglets fed ferric citrate performed significantly better than animals fed the negative control diet (containing only endogenous Fe) and those fed inorganic forms of Fe. Moreover, piglets fed ferric citrate demonstrated improved Fe digestibility and improved oxidative status. Altogether, these findings show that ferric citrate is a safe and easily digestible source of dietary Fe for broilers and piglets. creator: Klaus Männer creator: Hannah Lester creator: Eliana Henriquez-Rodriguez uri: https://doi.org/10.7717/peerj.12636 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2021 Männer et al. title: Impact of climatic conditions projected at the World Cup in Qatar 2022 on repeated maximal efforts in soccer players link: https://peerj.com/articles/12658 last-modified: 2021-12-22 description: This study aimed to investigate the relationship between the climatic conditions predicted for the 2022 FIFA World Cup in Qatar and the capacity for repeated maximum effort (RSA), of soccer players. Twenty-four semi-professional soccer players participated in the study. The exercise test consisted of ten 6-second maximal efforts on a cycloergometer. A 90-second passive rest interval was used. Mechanical parameters were recorded in each repetition, and biochemical parameters at rest and even repetitions. The test was performed in a Weiss Technik WK-26 climate chamber under two different conditions: (1) thermoneutral (TNC - 20.5 °C; 58.7% humidity); (2) predicted for the 2022 World Cup in Qatar (QSC - 28.5 ± 1.92 °C; 58.7 ± 8.64% humidity). Significantly higher mean maximum power values were recorded in the second repetition under QSC conditions (1731,8 ± 214,4 W) (p = 0.025). A significantly longer time to reach maximum power was also recorded under TNC conditions compared to QSC conditions in repetition 2 (1,32 ± 0,33 s), (1,05 ± 0,29 s) (p = 0.016) and 6 (1,41 ± 0,48 s), (1,17 ± 0,25) (p = 0.036). There was a significantly higher rate of power loss, between repetition 2 (p = 0.023) and 4 (p = 0.043) under QSC conditions, compared to TNC. Considering the biochemical parameters, a significantly higher pO2 concentration was registered under QSC conditions in the 10th repetition (p = 0.006). The ambient temperature during exercise should be taken into account to determine the anaerobic exercise capacity of the athletes. At higher temperatures, there is a greater capacity for maximal effort, in terms of maximal power achieved, but with a greater decrease in performance. creator: Wiktor Chodor creator: Paweł Chmura creator: Jan Chmura creator: Marcin Andrzejewski creator: Ewa Jówko creator: Tomasz Buraczewski creator: Adrian Drożdżowski creator: Andrzej Rokita creator: Marek Konefał uri: https://doi.org/10.7717/peerj.12658 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2021 Chodor et al. title: A taxonomic outline of the Poecilimon affinis complex (Orthoptera) using the geometric morphometric approach link: https://peerj.com/articles/12668 last-modified: 2021-12-22 description: The genus Poecilimon contains 145 species, widely distributed in the Palaearctic, among which the Poecilimon ornatus group has the greatest diversity in the Balkans. Despite several revisions of the genus, the systematics of the species group, and in particular, of the taxa associated with the species Poecilimon affinis, is still unsolved. Due to morphological similarity, P. affinis with its subspecies, P. nonveilleri and P. pseudornatus form the Poecilimon affinis complex. The aim of this study is to test the hypotheses of an outlined species complex, namely the P. affinis complex, within the P. ornatus group using morphological data. Geometric analysis was conducted to explore variation in the structure of the male tegmen, ovipositor, male cercus, and male pronotum. The number of teeth and stridulatory file measurements provided additional information on morphological variation within the complex. A phylogenetic tree based on the cytochrome c oxidase subunit I gene (COI) was used for comparison with the morphological data. Canonical variate analysis showed that male tegmen and male cercus are good morphostructures to distinguish the taxa belonging to the P. affinis complex from other species in the P. ornatus group. This may confirm our assumption for the designation of the P. affinis complex. The results of the principal component analysis of stridulatory file measurements, molecular data, and CVA of the ovipositor suggest adding two additional species to the complex: P. ornatus and P. hoelzeli. creator: Maciej Kociński creator: Beata Grzywacz creator: Georgi Hristov creator: Dragan Chobanov uri: https://doi.org/10.7717/peerj.12668 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2021 Kociński et al. title: Transcriptome analysis of transgenic apple fruit overexpressing microRNA172 reveals candidate transcription factors regulating apple fruit development at early stages link: https://peerj.com/articles/12675 last-modified: 2021-12-22 description: BackgroundMicroRNA172 (miR172) has been proven to be critical for fruit growth, since elevated miR172 activity blocks the growth of apple (Malus x domestica Borkh.) fruit. However, it is not clear how overexpression of miR172 affects apple fruit developmental processes.MethodsTo answer this question, the present study, analyzed global transcriptional changes in miR172-overexpressing (miR172OX) and nongenetically modified wild-type (WT) apple fruit at two developmental stages and in different fruit tissues via RNA-seq. In addition, two cultivars, ‘Hanfu’ and ‘M9’, which have naturally fruit size variation, were included to identify miR172-dependent DEGs. qRT–PCRwas used to verify the reliability of our RNA-seq data.ResultsOverexpression of miR172 altered the expression levels of many cell proliferation- and cell expansion-related genes. Twenty-four libraries were generated, and 10,338 differentially expressed genes (DEGs) were detected between miR172OX and WT fruit tissues. ‘Hanfu’ and ‘M9’ are two common cultivars that bear fruit of different sizes (250 g and 75 g, respectively). Six libraries were generated, and 3,627 DEGs were detected between ‘Hanfu’ and ‘M9’. After merging the two datasets, 6,888 candidate miR172-specific DEGs were identified. The potential networks associated with fruit size triggered traits were defined among genes belonging to the families of hormone synthesis, signaling pathways, and transcription factors. Our comparative transcriptome analysis provides insights into transcriptome responses to miR172 overexpression in apple fruit and a valuable database for future studies to validate functional genes and elucidate the fruit developmental mechanisms in apple. creator: Zhe Zhou creator: Yanmin Zhu creator: Hengtao Zhang creator: Ruiping Zhang creator: Qiming Gao creator: Tiyu Ding creator: Huan Wang creator: Zhenli Yan creator: Jia-Long Yao uri: https://doi.org/10.7717/peerj.12675 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2021 Zhou et al. title: A review of starch biosynthesis in cereal crops and its potential breeding applications in rice (Oryza Sativa L.) link: https://peerj.com/articles/12678 last-modified: 2021-12-22 description: Starch provides primary storage of carbohydrates, accounting for approximately 85% of the dry weight of cereal endosperm. Cereal seeds contribute to maximum annual starch production and provide the primary food for humans and livestock worldwide. However, the growing demand for starch in food and industry and the increasing loss of arable land with urbanization emphasizes the urgency to understand starch biosynthesis and its regulation. Here, we first summarized the regulatory signaling pathways about leaf starch biosynthesis. Subsequently, we paid more attention to how transcriptional factors (TFs) systematically respond to various stimulants via the regulation of the enzymes during starch biosynthesis. Finally, some strategies to improve cereal yield and quality were put forward based on the previous reports. This review would collectively help to design future studies on starch biosynthesis in cereal crops. creator: Ruiqing Li creator: Wenyin Zheng creator: Meng Jiang creator: Huali Zhang uri: https://doi.org/10.7717/peerj.12678 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2021 Li et al. title: An estimate of the area of occupancy and population size of Brachycephalus tridactylus (Anura: Brachycephalidae) to reassess its conservation status, with a proposal for conservation measures link: https://peerj.com/articles/12687 last-modified: 2021-12-22 description: BackgroundWe are experiencing a global crisis in conservation, which has led to the prioritization of targets, such as nations, regions, and animal groups, which are necessary while resources are disputed. Brazil is a priority not only because of its megadiversity, high rates of endemism, and frequent descriptions of new species but also because of its high levels of deforestation. Among the species groups prioritized for conservation is the anurans (Amphibia: Anura), the population of which is severely declining. One group of anurans is the genus Brachycephalus, which includes 37 endemic species in the Brazilian Atlantic Rainforest. Some of these species have highly restricted distributions (<100 ha). Thirty new species have been described since 2000, and 55.3% of all species are threatened with extinction. Brachycephalus tridactylus was only recently described and remains restricted to its type locality. Because of its reduced geographical distribution (0.41 km2), it has been proposed to be considered as Vulnerable. The objective of this study is to reevaluate the conservation status of Brachycephalus tridactylus and propose conservation measures.MethodsWe searched for new populations during 2016–2020, evaluated in loco impacts and potential impacts on the species’ population, and performed an analysis of the density of this population and estimated its size. International Union for Conservation of Nature (IUCN) criteria were used to assess the conservation status of the species.ResultsWe recorded the species in seven new localities (from 715–1,140 m above sea level) in the state of São Paulo up to 33 km from the type locality of the species (in state of Paraná). We estimated the area of occupancy as 148.44 km2, densities as one calling male per 4.05 m2 and 130.00 m2, and a total population size of 4,429,722 adult individuals. Based on our finding, we proposed three lines of management: (1) formation of fire brigades, (2) management of residents’ mules in the conservation unit and surrounding areas, and (3) management of degraded areas. We recommend changing the species’ conservation status from Vulnerable to Endangered because of its fragmented distribution and decline in the area of occupancy and in the quality of its habitat. Our results have expanded the species previous geographic distribution and delimited areas without previous records. Our estimates of population density and size are in accordance with those verified for congeners. The conservation of this species benefits the environments and other species that inhabit them, being, therefore, strategic for receiving conservation actions that will spread throughout the ecosystem. creator: Marcos R. Bornschein creator: Júnior Nadaline creator: Luiz Fernando Ribeiro creator: Giovanna Sandretti-Silva creator: Maria Fernanda Ferreira Rivas creator: Bruno de Morais Guerra creator: Larissa Teixeira uri: https://doi.org/10.7717/peerj.12687 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2021 Bornschein et al. title: Genome-wide identification and characterization of SPX-domain-containing protein gene family in Solanum lycopersicum link: https://peerj.com/articles/12689 last-modified: 2021-12-22 description: The SYG1, PHO81, and XPR1 (SPX) domain is named after the suppressor of yeast gpa1 (Syg1), yeast phosphatase (Pho81) and the human Xenotropic and Polytrophic Retrovirus receptor1 (XPR1). SPX-domain-containing proteins play pivotal roles in maintaining phosphate ions (Pi) homeostasis in plant. This study was to genome-wide identification and analysis of Solanum lycopersicum SPX-domain-containing protein gene family. The Solanum lycopersicum genome contains 19 SPX-domain-containing protein genes. These SPX-domain-containing protein genes were located in seven of the 12 chromosomes. According to the different conserved domains, the proteins encoded by those genes could be divided into four SPX-domain-containing protein families, which included SPX Family, SPX-ERD1/XPR1/SYG1(SPX-EXS) Family, SPX-Major Facilitator Superfamily (SPX-MFS) Family and SPX-Really Interesting New Gene (SPX-RING) Family. Phylogenetic analysis of SPX-domain-containing protein genes in Arabidopsis thaliana, Solanum tuberosum, Capsicum annuum and Solanum lycopersicum classified these genes into eight clades. Expression profiles derived from transcriptome (RNA-seq) data analysis showed 19 SPX-domain-containing protein genes displayed various expression patterns. SPX-domain-containing protein may play different roles in phosphate nutrition of Solanum lycopersicum different tissues and development stages. And, this study can provide the selection of candidate genes for functional research and genome editing in Solanum lycopersicum phosphate ions (Pi) nutrition. creator: Chunwei Li creator: Qiuye You creator: Panfeng Zhao uri: https://doi.org/10.7717/peerj.12689 license: https://creativecommons.org/licenses/by/4.0/ rights: © 2021 Li et al. title: Transcriptomic identification of HBx-associated hub genes in hepatocellular carcinoma link: https://peerj.com/articles/12697 last-modified: 2021-12-22 description: BackgroundHepatocellular carcinoma (HCC) is one of the most common malignancies around the world. Among the risk factors involved in liver carcinogenesis, hepatitis B virus (HBV) X protein (HBx) is considered to be a key regulator in hepatocarcinogenesis. Whether HBx promotes or protects against HCC remains controversial, therefore exploring new HBx-associated genes is still important.MethodsHBx was overexpressed in HepG2, HepG2.2.15 and SMMC-7721 cell lines, primary mouse hepatocytes and livers of C57BL/6N mice. High-throughput RNA sequencing profiling of HepG2 cells with HBx overexpression and related differentially-expressed genes (DEGs), pathway enrichment analysis, protein-protein interaction networks (PPIs), overlapping analysis were conducted. In addition, Gene Expression Omnibus (GEO) and proteomic datasets of HBV-positive HCC datasets were used to verify the expression and prognosis of selected DEGs. Finally, we also evaluated the known oncogenic role of HBx by oncogenic array analysis.ResultsA total of 523 DEGs were obtained from HBx-overexpressing HepG2 cells. Twelve DEGs were identified and validated in cells transiently transfected with HBx and three datasets of HBV-positive HCC transcription profiles. In addition, using the Kaplan-Meier plotter database, the expression levels of the twelve different genes were further analyzed to predict patient outcomes.ConclusionAmong the 12 identified HBx-associated hub genes, HBV-positive HCC patients expressing ARG1 and TAT showed a good overall survival (OS) and relapse-free survival (RFS). Thus, ARG1 and TAT expression could be potential prognostic markers. creator: Zhengzhong Ni creator: Jun Lu creator: Weiyi Huang creator: Hanif Khan creator: Xuejun Wu creator: Danmei Huang creator: Ganggang Shi creator: Yongdong Niu creator: Haihua Huang uri: https://doi.org/10.7717/peerj.12697 license: https://creativecommons.org/licenses/by/4.0/ rights: ©2021 Ni et al.