bluuebunny/crossref_metadata_2025 huggingface dataset:
Load-power relationship in older adults: The influence of maximal mean and peak power values and their associations with lower and upper-limb functional capacity
Authors: Marques Diogo Luís , Neiva Henrique Pereira , Marinho Daniel Almeida , Pires Ivan Miguel , Nunes Célia , Marques Mário Cardoso
Published: September 2022

Identifying the relative loads (%1RM) that maximize power output (Pmax-load) in resistance exercises can help design interventions to optimize muscle power in older adults. Moreover, examining the maximal mean power (MPmax) and peak power (PPmax) values (Watts) would allow an understanding of their differences and associations with functionality markers in older adults. Therefore, this research aimed to 1) analyze the load-mean and peak power relationships in the leg press and chest press in older adults, 2) examine the differences between mean Pmax-load (MPmax-load) and peak Pmax-load (PPmax-load) within resistance exercises, 3) identify the differences between resistance exercises in MPmax-load and PPmax-load, and 4) explore the associations between MPmax and PPmax in the leg press and chest press with functional capacity indicators. Thirty-two older adults (79.3 ± 7.3 years) performed the following tests: medicine ball throw (MBT), five-repetition sit-to-stand (STS), 10-m walking (10 W), and a progressive loading test in the leg press and chest press. Quadratic regressions analyzed 1) the load-mean and peak power relationships and identified the MPmax-load, MPmax, PPmax-load, and PPmax in both exercises, 2) the associations between MPmax and PPmax in the chest press with MBT, and 3) the associations between MPmax and PPmax in the leg press with STSpower and 10Wvelocity. In the leg press, the MPmax-load was ∼66% 1RM, and the PPmax-load was ∼62% 1RM, both for women and men (p > 0.05). In the chest press, the MPmax-load was ∼62% 1RM, and the PPmax-load was ∼56% 1RM, both for women and men (p > 0.05). There were differences between MPmax-load and PPmax-load within exercises (p < 0.01) and differences between exercises in MPmax-load and PPmax-load (p < 0.01). The MPmax and PPmax in the chest press explained ∼48% and ∼52% of the MBT-1 kg and MBT-3 kg variance, respectively. In the leg press, the MPmax and PPmax explained ∼59% of STSpower variance; however, both variables could not explain the 10Wvelocity performance (r2 ∼ 0.02). This study shows that the Pmax-load is similar between sexes, is resistance exercise-specific, and varies within exercises depending on the mechanical power variable used in older adults. Furthermore, this research demonstrates the influence of the MBT as an upper-limb power marker in older adults.
Melatonin Potentiates Exercise-Induced Increases in Skeletal Muscle PGC-1α and Optimizes Glycogen Replenishment
Authors: Faria Vinícius Silva , Manchado-Gobatto Fúlvia Barros , Scariot Pedro Paulo Menezes , Zagatto Alessandro Moura , Beck Wladimir Rafael
Published: September 2022

Compelling evidence has demonstrated the effect of melatonin on exhaustive exercise tolerance and its modulatory role in muscle energy substrates at the end of exercise. In line with this, PGC-1α and NRF-1 also seem to act on physical exercise tolerance and metabolic recovery after exercise. However, the literature still lacks reports on these proteins after exercise until exhaustion for animals treated with melatonin. Thus, the aim of the current study was to determine the effects of acute melatonin administration on muscle PGC-1α and NRF-1, and its modulatory role in glycogen and triglyceride contents in rats subjected to exhaustive swimming exercise at an intensity corresponding to the anaerobic lactacidemic threshold (iLAn). In a randomized controlled trial design, thirty-nine Wistar rats were allocated into four groups: control (CG = 10), rats treated with melatonin (MG = 9), rats submitted to exercise (EXG = 10), and rats treated with melatonin and submitted to exercise (MEXG = 10). Forty-eight hours after the graded exercise test, the animals received melatonin (10 mg/kg) or vehicles 30 min prior to time to exhaustion test in the iLAn (tlim). Three hours after tlim the animals were euthanized, followed by muscle collection for specific analyses: soleus muscles for immunofluorescence, gluteus maximus, red and white gastrocnemius for the assessment of glycogen and triglyceride contents, and liver for the measurement of glycogen content. Student t-test for independent samples, two-way ANOVA, and Newman keuls post hoc test were used. MEXG swam 120.3% more than animals treated with vehicle (EXG; p < 0.01). PGC-1α and NRF-1 were higher in MEXG with respect to the CG (p < 0.05); however, only PGC-1α was higher for MEXG when compared to EXG. Melatonin reduced the triglyceride content in gluteus maximus, red and white gastrocnemius (F = 6.66, F = 4.51, and F = 6.02, p < 0.05). The glycogen content in red gastrocnemius was higher in MEXG than in CG (p = 0.01), but not in EXG (p > 0.05). In conclusion, melatonin was found to enhance exercise tolerance, potentiate exercise-mediated increases in PGC-1α, decrease muscle triglyceride content and increase muscle glycogen 3 h after exhaustive exercise, rapidly providing a better cellular metabolic environment for future efforts.
A potential role of p75NTR in the regulation of circadian rhythm and incremental growth lines during tooth development
Authors: Yuan Hongyan , Xie Bo , Yu Xia , Lin Cheng , Li Meng , Zhang Yixin , Zou Xuqiang , Lu Mingjie , Zhao Manzhu , Wen Xiujie
Published: September 2022

Objective: Tooth morphogenesis and the formation of hard tissues have been reported to be closely related to circadian rhythms. This study investigates the spatiotemporal expression and relationship of p75NTR with core clock genes, mineralization-related or odontogenesis-related genes, and aims to derive the potential role of p75NTR in regulating circadian rhythm and incrementality growth line formation during tooth development.

Materials and methods: The dynamic morphology of the rat dental germ was observed at seven stages (E14.5 d, E16.5 d, E18.5 d, P.N. 4 d, P.N. 7 d, P.N. 10 d, and P.N. 15 d). Next, the expressions of p75NTR and other target factors were traced. The ectomesenchymal stem cells (EMSCs) were isolated from the E18.5d rat dental germs and synchronized using 50% of fetal bovine serum. Then, they were cultured in light/light (L.L.), dark/dark (D.D.), and light/dark (L.D.) conditions for 48 h. The total RNA was collected every 4 h, and the circadian rhythm dynamics of target factors were observed. To reveal the mechanism further, p75NTR was down-regulated in p75NTRExIII−/− mice and up-regulated in immortalized mouse dental apical papilla progenitor cells. The change tendencies of other target factors were also detected.

Results: The clock genes Bmal1, Clock, Per1, and Per2 were all expressed in tooth germs before the formation of dental hard tissues and demonstrated a regular oscillating expression pattern in EMSCs from dental germs. Their expression was affected by the L.D. stimulus, and most of them were promoted by D.D. conditions. p75NTR presented a similar expression pattern and a positive or negative relationship with most clock genes, mineralization-related and odontogenesis-related factors, such as brain and muscle ARNT-like protein-1 (Bmal1), runt-related transcription factor 2 (Runx2), alkaline phosphatase (ALP), MSH-like 1 (MSX1), dentin matrix acidic phosphoprotein 1 (Dmp1), and dentin sialophosphoprotein (Dspp). Moreover, the arrangement, morphology, and even boundary in pre-odontoblast/pre-ameloblast layers were disordered in the p75NTRExIII−/− mice.

Conclusion: Circadian rhythm was found to affect tooth development. p75NTR might play a crucial role in regulating clock genes in the mineralization and formation of the dental hard tissues. p75NTR is actively involved in the odontoblast-ameloblast junction and cell polarity establishment during tooth morphogenesis.
Radiation environment in exploration-class space missions and plants’ responses relevant for cultivation in Bioregenerative Life Support Systems
Authors: De Micco Veronica , Arena Carmen , Di Fino Luca , Narici Livio
Published: September 2022

For deep space exploration, radiation effects on astronauts, and on items fundamental for life support systems, must be kept under a pre-agreed threshold to avoid detrimental outcomes. Therefore, it is fundamental to achieve a deep knowledge on the radiation spatial and temporal variability in the different mission scenarios as well as on the responses of different organisms to space-relevant radiation. In this paper, we first consider the radiation issue for space exploration from a physics point of view by giving an overview of the topics related to the spatial and temporal variability of space radiation, as well as on measurement and simulation of irradiation, then we focus on biological issues converging the attention on plants as one of the fundamental components of Bioregenerative Life Support Systems (BLSS). In fact, plants in BLSS act as regenerators of resources (i.e. oxygen production, carbon dioxide removal, water and wastes recycling) and producers of fresh food. In particular, we summarize some basic statements on plant radio-resistance deriving from recent literature and concentrate on endpoints critical for the development of Space agriculture. We finally indicate some perspective, suggesting the direction future research should follow to standardize methods and protocols for irradiation experiments moving towards studies to validate with space-relevant radiation the current knowledge. Indeed, the latter derives instead from experiments conducted with different radiation types and doses and often with not space-oriented scopes.
A chromosome-level genome assembly of the Chinese cork oak (Quercus variabilis)
Authors: Han Biao , Wang Longxin , Xian Yang , Xie Xiao-Man , Li Wen-Qing , Zhao Ye , Zhang Ren-Gang , Qin Xiaochun , Li De-Zhu , Jia Kai-Hua
Published: September 2022

Quercus variabilis(Fagaceae) is an ecologically and economically important deciduous broadleaved tree species native to and widespread in East Asia. It is a valuable woody species and an indicator of local forest health, and occupies a dominant position in forest ecosystems in East Asia. However, genomic resources fromQ. variabilisare still lacking. Here, we present a high-qualityQ. variabilisgenome generated by PacBio HiFi and Hi-C sequencing. The assembled genome size is 787 Mb, with a contig N50 of 26.04 Mb and scaffold N50 of 64.86 Mb, comprising 12 pseudo-chromosomes. The repetitive sequences constitute 67.6% of the genome, of which the majority are long terminal repeats, accounting for 46.62% of the genome. We usedab initio, RNA sequence-based and homology-based predictions to identify protein-coding genes. A total of 32,466 protein-coding genes were identified, of which 95.11% could be functionally annotated. Evolutionary analysis showed thatQ. variabiliswas more closely related toQ. suberthan toQ. lobataorQ. robur.We found no evidence for species-specific whole genome duplications inQuercusafter the species had diverged. This study provides the first genome assembly and the first gene annotation data forQ. variabilis.These resources will inform the design of further breeding strategies, and will be valuable in the study of genome editing and comparative genomics in oak species.
Nitrogen metabolic rate and differential ammonia volatilization regulate resistance against opportunistic fungus Alternaria alternata in tobacco
Authors: Yang Zhixiao , Chen Yi , Wang Yi , Xia Haiqian , Zheng Shaoqing , Xie Shengdong , Cao Yi , Liu Jiemin , Sehar Shafaque , Lin Yingchao , Guo Yushuang , Shamsi Imran Haider
Published: September 2022

Nutritional correlations between plants and pathogens can crucially affect disease severity. As an essential macronutrient, the availability of nitrogen (N) and the types of N content play a fundamental part not only in energy metabolism and protein synthesis but also in pathogenesis. However, a direct connection has not yet been established between differences in the level of resistance and N metabolism. Pertinently, former studies hold ammonia (NH3) accountable for the development of diseases in tobacco (Nicotiana tabacum L.) and in some post-harvest fruits. With a purpose of pinpointing the function of NH3 volatilization on Alternaria alternata (Fries) Keissl pathogenesis and its correlation with both N metabolism and resistance differences to Alternaria alternata infection in tobacco, leaf tissue of two tobacco cultivars with susceptibility (Changbohuang; CBH), or resistance (Jingyehuang; JYH) were analyzed apropos of ammonia compensation point, apoplastic NH4+ concentration, pH value as well as activities of key enzymes and N status. At the leaf age of 40 to 60 d, the susceptible cultivar had a significantly higher foliar apoplastic ammonium (NH4+) concentration, pH value and NH3 volatilization potential compared to the resistant one accompanied by a significant reduction in glutamine synthetase (GS), which in particular was a primary factor causing the NH3 volatilization. The NH4+ concentration in CBH was 1.44 times higher than that in JYH, and CBH had NH3 compensation points that were 7.09, 6.15 and 4.35-fold higher than those of JYH at 40, 50 and 60 d, respectively. Moreover, the glutamate dehydrogenase (GDH) activity had an upward tendency related to an increased NH4+ accumulation in both leaf tissues and apoplast but not with the NH3 compensation point. Collectively, our results strongly suggest that the accumulation of NH3 volatilization, rather than NH4+ and total N, was the primary factor inducing the Alternaria alternata infection in tobacco. Meanwhile, the susceptible cultivar was characterized by a higher N re-transfer ability of NH3 volatilization, in contrast to the disease–resistant cultivar, and had a stronger capability of N assimilation and reutilization. This study provides a deeper understanding of the pathogenicity mechanism induced by Alternaria alternata, which is useful for breeding Alternaria alternata-resistant varieties of tobacco, at the same time, our research is also conducive to control tobacco brown spot caused by Alternaria alternata in the field.
Chromosome-scale genome assembly of Camellia sinensis combined with multi-omics provides insights into its responses to infestation with green leafhoppers
Authors: Wang Fen , Zhang Baohui , Wen Di , Liu Rong , Yao Xinzhuan , Chen Zhi , Mu Ren , Pei Huimin , Liu Min , Song Baoxing , Lu Litang
Published: September 2022

The tea plant (Camellia sinensis) is an important economic crop, which is becoming increasingly popular worldwide, and is now planted in more than 50 countries. Tea green leafhopper is one of the major pests in tea plantations, which can significantly reduce the yield and quality of tea during the growth of plant. In this study, we report a genome assembly for DuyunMaojian tea plants using a combination of Oxford Nanopore Technology PromethION™ with high-throughput chromosome conformation capture technology and used multi-omics to study how the tea plant responds to infestation with tea green leafhoppers. The final genome was 3.08 Gb. A total of 2.97 Gb of the genome was mapped to 15 pseudo-chromosomes, and 2.79 Gb of them could confirm the order and direction. The contig N50, scaffold N50 and GC content were 723.7 kb, 207.72 Mb and 38.54%, respectively. There were 2.67 Gb (86.77%) repetitive sequences, 34,896 protein-coding genes, 104 miRNAs, 261 rRNA, 669 tRNA, and 6,502 pseudogenes. A comparative genomics analysis showed that DuyunMaojian was the most closely related to Shuchazao and Yunkang 10, followed by DASZ and tea-oil tree. The multi-omics results indicated that phenylpropanoid biosynthesis, α-linolenic acid metabolism, flavonoid biosynthesis and 50 differentially expressed genes, particularly peroxidase, played important roles in response to infestation with tea green leafhoppers (Empoasca vitis Göthe). This study on the tea tree is highly significant for its role in illustrating the evolution of its genome and discovering how the tea plant responds to infestation with tea green leafhoppers will contribute to a theoretical foundation to breed tea plants resistant to insects that will ultimately result in an increase in the yield and quality of tea.
Genome-wide identification of three-amino-acid-loop-extension gene family and their expression profile under hormone and abiotic stress treatments during stem development of Prunus mume
Authors: Yang Qingqing , Yuan Cunquan , Cong Tianci , Wang Jia , Zhang Qixiang
Published: September 2022

Transcription factors encoded by the three-amino-acid-loop-extension (TALE) gene family play a key role in regulating plant growth and development, and are involved in plant hormone regulatory pathways and responses to various environmental stresses. Researchers are currently studying TALE genes in different species, but Prunus mumeTALE genes have not yet been studied. Therefore, based on the P. mume genome, we found a total of 23 TALE gene family members, which were distributed on eight chromosomes. TALE genes contained the characteristic domains of this family, and could be divided into KNOTTED-like homeobox (KNOX) subfamily and BEL1-like homeobox (BELL) subfamily. They can form heterodimers with each other. Fragment duplication and tandem duplication events were the main reasons for the expansion of P. mumeTALE gene family members and the TALE genes were selected by different degrees of purification. The inter-species collinearity analysis showed that the relationship between P. mume and other four Prunus species was consistent with the distance of origin. Eleven members of P. mumeTALE genes were specifically highly expressed in stem, mainly at the early stage of stem development. The cis-element analysis showed that the promoter of P. mumeTALE genes contained a variety of hormone and abiotic stress response elements, and four TALE genes responded to two kinds of abiotic stresses and four kinds of hormones at the early stage of stem development. In conclusion, this study lays a foundation to explore the role of TALE gene family in P. mume growth and development.
Identification of gene family members and a key structural variation reveal important roles of OVATE genes in regulating tea (Camellia sinensis) leaf development
Authors: An Yanlin , Xia Xiaobo , Jing Tingting , Zhang Feng
Published: September 2022

OVATE genes are a new class of transcriptional repressors with important regulatory roles in plant growth and development. Through genome-wide analysis of the OVATE gene family of tea plants, 26 and 13 family members were identified in cultivated and ancient tea plants, respectively. Syntenic results showed that OVATE gene family in cultivated tea plants may have experienced a special expansion event. Based on phylogenetic tree analysis, all OVATE genes were divided into four groups, and the third group had the largest number, reaching 16. Transcriptome data from different organs and populations indicated that many OVATE family members were highly expressed in young shoots and leaves, and their expression levels gradually decreased as tea leaves developed. Finally, the expression trends of the six key candidate genes were verified by RT-qPCR, which were consistent with the transcriptome results, indicating that the ovate gene family plays an important role in regulating the process of tea leaf development. In addition, we identified a key structural variation with a length of 184 bp, and the population genotyping showed that it was closely related to the area of tea leaves. Our research provides an important clue for further exploring the function of ovate gene family in tea plants and the development mechanism of tea leaves.
First genetic maps development and QTL mining in Ranunculus asiaticus L. through ddRADseq
Authors: Martina Matteo , Acquadro Alberto , Gulino Davide , Brusco Fabio , Rabaglio Mario , Portis Ezio , Lanteri Sergio
Published: September 2022

Persian Buttercup (Ranunculus asiaticus L.; 2x=2n=16; estimated genome size: 7.6Gb) is an ornamental and perennial crop native of Asia Minor and Mediterranean basin, marketed both as cut flower or potted plant. Currently new varieties are developed by selecting plants carrying desirable traits in segregating progenies obtained by controlled mating, which are propagated through rhizomes or micro-propagated in vitro. In order to escalate selection efficiency and respond to market requests, more knowledge of buttercup genetics would facilitate the identification of markers associated with loci and genes controlling key ornamental traits, opening the way for molecular assisted breeding programs. Reduced-representation sequencing (RRS) represents a powerful tool for plant genotyping, especially in case of large genomes such as the one of buttercup, and have been applied for the development of high-density genetic maps in several species. We report on the development of the first molecular-genetic maps in R. asiaticus based on of a two-way pseudo-testcross strategy. A double digest restriction-site associated DNA (ddRAD) approach was applied for genotyping two F1 mapping populations, whose female parents were a genotype of a so called ‘ponpon’ and of a ‘double flower’ varieties, while the common male parental (‘Cipro’) was a genotype producing a simple flower. The ddRAD generated a total of ~2Gb demultiplexed reads, resulting in an average of 8,3M reads per line. The sstacks pipeline was applied for the construction of a mock reference genome based on sequencing data, and SNP markers segregating in only one of the parents were retained for map construction by treating the F1 population as a backcross. The four parental maps (two of the female parents and two of the common male parent) were aligned with 106 common markers and 8 linkage groups were identified, corresponding to the haploid chromosome number of the species. An average of 586 markers were associated with each parental map, with a marker density ranging from 1 marker/cM to 4.4 markers/cM. The developed maps were used for QTL analysis for flower color, leading to the identification of major QTLs for purple pigmentation. These results contribute to dissect on the genetics of Persian buttercup, enabling the development of new approaches for future varietal development.
Wind loss model for the thick canopies of orchard trees based on accurate variable spraying
Authors: Gu Chenchen , Zou Wei , Wang Xiu , Chen Liping , Zhai Changyuan
Published: September 2022

Variable application by wind is an efficient application technology recommended by the Food and Agriculture Organization (FAO) of the United Nations that can effectively improve the deposition effect of liquid medicine in a canopy and reduce droplet drift. In view of the difficulty of modelling wind forces in orchard tree canopies and the lack of a wind control model, the wind loss model for a canopy was studied. First, a three-dimensional wind measurement test platform was built for an orchard tree canopy. The orchard tree was located in three-dimensional space, and the inner leaf areas of the orchard tree canopy and the wind force in different areas were measured. Second, light detection and ranging (LiDAR) point cloud data of the orchard tree canopy were obtained by LiDAR scanning. Finally, classic regression, partial least squares regression (PLSR), and back propagation (BP) neural network algorithms were used to build wind loss models in the canopy. The research showed that the BP neural network algorithm can significantly improve the fitting accuracy of the model. Under different fan speeds of 1,381 r/min, 1,502 r/min, and 1,676 r/min, the coefficient of determination (R2) of the model were 81.78, 72.85, and 69.20%, respectively, which were 19.38, 7.55, and 12.3% higher than those of the PLSR algorithm and 21.48, 22.25, and 24.3% higher than those of multiple regression analysis. The comparison showed that the BP neural network algorithm obtains the highest model accuracy, but because the model is not intuitive, PLSR has the advantages of intuitive and simple models in the three algorithms. In practical applications, the wind loss model based on a BP neural network or PLSR can be selected according to the operational requirements and software and hardware conditions. This study can provide a basis for wind control in precise variable spraying and promote the development of wind control technologies.
A chromosome-scale genome assembly of Quercus gilva: Insights into the evolution of Quercus section Cyclobalanopsis (Fagaceae)
Authors: Zhou Xia , Liu Na , Jiang Xiaolong , Qin Zhikuang , Farooq Taimoor Hassan , Cao Fuliang , Li He
Published: September 2022

Quercus gilva is an ecologically and economically important species of Quercus section Cyclobalanopsis and is a dominant species in evergreen broad-leaved forests in subtropical regions of East Asia. In the present study, we reported a high-quality chromosome-scale genome assembly of Q. gilva, the first reference genome for section Cyclobalanopsis, using the combination of Illumina and PacBio sequencing with Hi-C technologies. The assembled genome size of Q. gilva was 889.71 Mb, with a contig number of 773 and a contig N50 of 28.32 Mb. Hi-C scaffolding anchored 859.07 Mb contigs (96.54% of the assembled genome) onto 12 pseudochromosomes, with a scaffold N50 of 70.35 Mb. A combination of de novo, homology-based, and transcript-based predictions predicted a final set of 36,442 protein-coding genes distributed on 12 pseudochromosomes, and 97.73% of them were functionally annotated. A total of 535.64 Mb (60.20%) of repetitive sequences were identified. Genome evolution analysis revealed that Q. gilva was most closely related to Q. suber and they diverged at 40.35 Ma, and Q. gilva did not experience species-specific whole-genome duplication in addition to the ancient gamma (γ) whole-genome triplication event shared by core eudicot plants. Q. gilva underwent considerable gene family expansion and contraction, with 598 expanded and 6,509 contracted gene families detected. The first chromosome-scale genome of Q. gilva will promote its germplasm conservation and genetic improvement and provide essential resources for better studying the evolution of Quercus section Cyclobalanopsis.
Molecular basis of nitrogen starvation-induced leaf senescence
Authors: Sakuraba Yasuhito
Published: September 2022

Nitrogen (N), a macronutrient, is often a limiting factor in plant growth, development, and productivity. To adapt to N-deficient environments, plants have developed elaborate N starvation responses. Under N-deficient conditions, older leaves exhibit yellowing, owing to the degradation of proteins and chlorophyll pigments in chloroplasts and subsequent N remobilization from older leaves to younger leaves and developing organs to sustain plant growth and productivity. In recent years, numerous studies have been conducted on N starvation-induced leaf senescence as one of the representative plant responses to N deficiency, revealing that leaf senescence induced by N deficiency is highly complex and intricately regulated at different levels, including transcriptional, post-transcriptional, post-translational and metabolic levels, by multiple genes and proteins. This review summarizes the current knowledge of the molecular mechanisms associated with N starvation-induced leaf senescence.
HbTGA1, a TGA Transcription Factor From Hevea brasiliensis, Regulates the Expression of Multiple Natural Rubber Biosynthesis Genes
Authors: Guo Dong , Li Hui-Liang , Zhu Jia-Hong , Wang Ying , Peng Shi-Qing
Published: September 2022

The TGA transcription factors are known to modulate the biosynthesis of secondary metabolites in plants. However, their regulatory function in natural rubber (NR) biosynthesis was not revealed in the rubber tree (Hevea brasiliensis). Here, 14 genes encoding TGA transcription factors (name HbTGA1-HbTGA14) were identified in the rubber tree. HbTGAs were differentially expressed in different tissues. HbTGA1 was expressed at its highest level in latex. We found specific in vitro and in vivo binding of the HbTGA1 protein with promoters of multiple NR biosynthesis genes (HbHMGS2, HbHMGR2, HbCPT6, HbCPT8, and HbSRPP2). The activation of the promoters of HbHMGS2 and HbCPT6 was significantly suppressed by HbTGA1, while the activities of promoters of HbHMGR2, HbCPT8, and HbSRPP2 were increased by HbTGA1. The promoter activities of HbHMGS2, HbHMGR2, HbCPT6, HbCPT8, and HbSRPP2 were significantly increased by HbTGA1 under jasmonate stress, while the promoter activities of HbHMGS2, HbHMGR2, HbCPT6, HbCPT8, and HbSRPP2 were also significantly increased by HbTGA1 under salicylic acid stress. The present study provides insights into the role of TGA transcription factors in regulating the expression of NR biosynthesis genes from H. brasiliensis.
Root system architecture for abiotic stress tolerance in potato: Lessons from plants
Authors: Zinta Rasna , Tiwari Jagesh Kumar , Buckseth Tanuja , Thakur Kanika , Goutam Umesh , Kumar Devendra , Challam Clarissa , Bhatia Nisha , Poonia Anuj K. , Naik Sharmistha , Singh Rajesh K. , Thakur Ajay K. , Dalamu Dalamu , Luthra Satish K. , Kumar Vinod , Kumar Manoj
Published: September 2022

The root is an important plant organ, which uptakes nutrients and water from the soil, and provides anchorage for the plant. Abiotic stresses like heat, drought, nutrients, salinity, and cold are the major problems of potato cultivation. Substantial research advances have been achieved in cereals and model plants on root system architecture (RSA), and so root ideotype (e.g., maize) have been developed for efficient nutrient capture to enhance nutrient use efficiency along with genes regulating root architecture in plants. However, limited work is available on potatoes, with a few illustrations on root morphology in drought and nitrogen stress. The role of root architecture in potatoes has been investigated to some extent under heat, drought, and nitrogen stresses. Hence, this mini-review aims to update knowledge and prospects of strengthening RSA research by applying multi-disciplinary physiological, biochemical, and molecular approaches to abiotic stress tolerance to potatoes with lessons learned from model plants, cereals, and other plants.
FERONIA-like receptor 1-mediated calcium ion homeostasis is involved in the immune response
Authors: Luo Xiao , Wang Long , Fu Yuefeng , Liu Qiqi , Chen Ge , Liu Yue , He Wei , Gao Aijun , Xu Jingbo , Deng Huafeng , Xing Junjie
Published: September 2022

Calcium (Ca2+) is the most abundant divalent cation in plants, and cellular levels of Ca2+, which functions as a nutrient and secondary messenger, play a critical role in plant immunity. In the present study, we found that FERONIA-like receptor 1 (FLR1) positively regulates Magnaporthe oryzae resistance and that expression of FLR1 is strongly induced in response to Ca2+ deficiency. In addition, the Ca content in the shoots of flr1 was lower than that in wild-type, and the M. oryzae-sensitive phenotype of the flr1 mutant was not rescued by exogenous application of Ca2+. Moreover, RNA sequencing revealed 2,697 differentially expressed genes (DEGs) in the flr1 mutant compared with wild-type, and some of these DEGs are involved in cellular metal ion homeostasis and transition metal ion homeostasis. Changes in expression of overlapping genes between the flr1 mutant and in plants under low-Ca2+ treatment were consistent in terms of direction, indicating that FLR1 is involved in Ca2+ homeostasis. In summary, we detected FLR1-mediated resistance to M. oryzae, a phenomenon associated with Ca2+ homeostasis.
Feature importance network reveals novel functional relationships between biological features in Arabidopsis thaliana
Authors: Ng Jonathan Wei Xiong , Chua Swee Kwang , Mutwil Marek
Published: September 2022

Understanding how the different cellular components are working together to form a living cell requires multidisciplinary approaches combining molecular and computational biology. Machine learning shows great potential in life sciences, as it can find novel relationships between biological features. Here, we constructed a dataset of 11,801 gene features for 31,522 Arabidopsis thaliana genes and developed a machine learning workflow to identify linked features. The detected linked features are visualised as a Feature Important Network (FIN), which can be mined to reveal a variety of novel biological insights pertaining to gene function. We demonstrate how FIN can be used to generate novel insights into gene function. To make this network easily accessible to the scientific community, we present the FINder database, available at finder.plant.tools.1
Long-term cultivation drives dynamic changes in the rhizosphere microbial community of blueberry
Authors: Che Jilu , Wu Yaqiong , Yang Hao , Wang Shaoyi , Wu Wenlong , Lyu Lianfei , Li Weilin
Published: September 2022

Rhizosphere microbial communities profoundly affect plant health, productivity, and responses to environmental stress. Thus, it is of great significance to comprehensively understand the response of root-associated microbes to planting years and the complex interactions between plants and rhizosphere microbes under long-term cultivation. Therefore, four rabbiteye blueberries (Vaccinium ashei Reade) plantations established in 1988, 2004, 2013, and 2017 were selected to obtain the dynamic changes and assembly mechanisms of rhizosphere microbial communities with the increase in planting age. Rhizosphere bacterial and fungal community composition and diversity were determined using a high-throughput sequencing method. The results showed that the diversity and structure of bacterial and fungal communities in the rhizosphere of blueberries differed significantly among planting ages. A total of 926 operational taxonomic units (OTUs) in the bacterial community and 219 OTUs in the fungal community were identified as the core rhizosphere microbiome of blueberry. Linear discriminant analysis effect size (LEfSe) analysis revealed 36 and 56 distinct bacterial and fungal biomarkers, respectively. Topological features of co-occurrence network analysis showed greater complexity and more intense interactions in bacterial communities than in fungal communities. Soil pH is the main driver for shaping bacterial community structure, while available potassium is the main driver for shaping fungal community structure. In addition, the VPA results showed that edaphic factors and blueberry planting age contributed more to fungal community variations than bacterial community. Notably, ericoid mycorrhizal fungi were observed in cultivated blueberry varieties, with a marked increase in relative abundance with planting age, which may positively contribute to nutrient uptake and coping with environmental stress. Taken together, our study provides a basis for manipulating rhizosphere microbial communities to improve the sustainability of agricultural production during long-term cultivation.
Type-A response regulators negatively mediate heat stress response by altering redox homeostasis in Arabidopsis
Authors: Jindal Sunita , Kerchev Pavel , Berka Miroslav , Černý Martin , Botta Halidev Krishna , Laxmi Ashverya , Brzobohatý Břetislav
Published: September 2022

Besides the long-standing role of cytokinins (CKs) as growth regulators, their current positioning at the interface of development and stress responses is coming into recognition. The current evidence suggests the notion that CKs are involved in heat stress response (HSR), however, the role of CK signaling components is still elusive. In this study, we have identified a role of the CK signaling components type-A Arabidopsis response regulators (ARRs) in HSR in Arabidopsis. The mutants of multiple type-A ARR genes exhibit improved basal and acquired thermotolerance and, altered response to oxidative stress in our physiological analyses. Through proteomics profiling, we show that the type-A arr mutants experience a ‘stress-primed’ state enabling them to respond more efficiently upon exposure to real stress stimuli. A substantial number of proteins that are involved in the heat-acclimatization process such as the proteins related to cellular redox status and heat shock, are already altered in the type-A arr mutants without a prior exposure to stress conditions. The metabolomics analyses further reveal that the mutants accumulate higher amounts of α-and γ-tocopherols, which are important antioxidants for protection against oxidative damage. Collectively, our results suggest that the type-A ARRs play an important role in heat stress response by affecting the redox homeostasis in Arabidopsis.
Transcriptome analysis reveals molecular mechanisms underlying salt tolerance in halophyte Sesuvium portulacastrum
Authors: Wang Dan , Yang Nan , Zhang Chaoyue , He Weihong , Ye Guiping , Chen Jianjun , Wei Xiangying
Published: September 2022

Soil salinity is an important environmental problem that seriously affects plant growth and crop productivity. Phytoremediation is a cost-effective solution for reducing soil salinity and potentially converting the soils for crop production. Sesuvium portulacastrum is a typical halophyte which can grow at high salt concentrations. In order to explore the salt tolerance mechanism of S. portulacastrum, rooted cuttings were grown in a hydroponic culture containing ½ Hoagland solution with or without addition of 400 mM Na for 21 days. Root and leaf samples were taken 1 h and 21 days after Na treatment, and RNA-Seq was used to analyze transcript differences in roots and leaves of the Na-treated and control plants. A large number of differentially expressed genes (DEGs) were identified in the roots and leaves of plants grown under salt stress. Several key pathways related to salt tolerance were identified through KEGG analysis. Combined with physiological data and expression analysis, it appeared that cyclic nucleotide gated channels (CNGCs) were implicated in Na uptake and Na+/H+ exchangers (NHXs) were responsible for the extrusion and sequestration of Na, which facilitated a balance between Na+ and K+ in S. portulacastrum under salt stress. Soluble sugar and proline were identified as important osmoprotectant in salt-stressed S. portulacastrum plants. Glutathione metabolism played an important role in scavenging reactive oxygen species. Results from this study show that S. portulacastrum as a halophytic species possesses a suite of mechanisms for accumulating and tolerating a high level of Na; thus, it could be a valuable plant species used for phytoremediation of saline soils.
Increasing evapotranspiration decouples the positive correlation between vegetation cover and warming in the Tibetan plateau
Authors: Dai Xue , Yu Zhongbo , Matheny Ashley M. , Zhou Wei , Xia Jun
Published: September 2022

Plant growth generally responds positively to an increase in ambient temperature. Hence, most Earth system models project a continuous increase in vegetation cover in the future due to elevated temperatures. Over the last 40 years, a considerable warming trend has affected the alpine ecosystem across the Tibetan Plateau. However, we found vegetation growth in the moderately vegetated areas of the plateau were negatively related to the warming temperatures, thus resulting in a significant degradation of the vegetative cover (LAI: slope = −0.0026 per year, p < 0.05). The underlying mechanisms that caused the decoupling of the relationship between vegetation growth and warming in the region were elaborated with the analysis of water and energy variables in the ecosystem. Results indicate that high temperatures stimulated evapotranspiration and increased the water consumption of the ecosystem (with an influence coefficient of 0.34) in these degrading areas, significantly reducing water availability (with an influence coefficient of −0.68) and limiting vegetation growth. Moreover, the negative warming effect on vegetation was only observed in the moderately vegetated areas, as evapotranspiration there predominantly occupied a larger proportion of available water (compared to the wet and highly vegetated areas) and resulted in a greater increase in total water consumption in a warmer condition (compared to dry areas with lower levels of vegetation cover). These findings highlight the risk of vegetation degradation in semi-arid areas, with the degree of vulnerability depending on the level of vegetation cover. Furthermore, results demonstrate the central role of evapotranspiration in regulating water stress intensity on vegetation under elevated temperatures.
Does polyploidy inhibit sex chromosome evolution in angiosperms?
Authors: He Li , Hörandl Elvira
Published: September 2022

Dioecy is rare in flowering plants (5–6% of species), but is often controlled genetically by sex-linked regions (SLRs). It has so far been unclear whether, polyploidy affects sex chromosome evolution, as it does in animals, though polyploidy is quite common in angiosperms, including in dioecious species. Plants could be different, as, unlike many animal systems, degenerated sex chromosomes, are uncommon in plants. Here we consider sex determination in plants and plant-specific factors, and propose that constraints created at the origin of polyploids limit successful polyploidization of species with SLRs. We consider the most likely case of a polyploid of a dioecious diploid with an established SLR, and discuss the outcome in autopolyploids and allopolyploids. The most stable system possibly has an SLR on just one chromosome, with a strongly dominant genetic factor in the heterogametic sex (e.g., xxxY male in a tetraploid). If recombination occurs with its homolog, this will prevent Y chromosome degeneration. Polyploidy may also allow for reversibility of multiplied Z or X chromosomes into autosomes. Otherwise, low dosage of Y-linked SLRs compared to their multiple homologous x copies may cause loss of reliable sex-determination at higher ploidy levels. We discuss some questions that can be studied using genome sequencing, chromosome level-assemblies, gene expression studies and analysis of loci under selection.
Overexpression of abscisic acid-insensitive gene ABI4 from Medicago truncatula, which could interact with ABA2, improved plant cold tolerance mediated by ABA signaling
Authors: Li Yinruizhi , Wang Mengdi , Guo Tao , Li Shuwen , Teng Ke , Dong Di , Liu Zhuocheng , Jia Chenyan , Chao Yuehui , Han Liebao
Published: September 2022

ABI4 is considered an important transcription factor with multiple regulatory functions involved in many biological events. However, its role in abiotic stresses, especially low-temperature-induced stress, is poorly understood. In this study, the MtABI4 gene was derived from M. truncatula, a widely used forage grass. Analysis of subcellular localization indicated that ABI4 was localized in the nucleus. Identification of expression characteristics showed that ABI4 was involved in the regulatory mechanisms of multiple hormones and could be induced by the low temperature. IP-MS assay revealed that MtABI4 protein could interact with xanthoxin dehydrogenase protein (ABA2). The two-hybrid yeast assay and the biomolecular fluorescence complementarity assay further supported this finding. Expression analysis demonstrated that overexpression of MtABI4 induced an increase in ABA2 gene expression both in M. truncatula and Arabidopsis, which in turn increased the ABA level in transgenic plants. In addition, the transgenic lines with the overexpression of MtABI4 exhibited enhanced tolerance to low temperature, including lower malondialdehyde content, electrical conductivity, and cell membrane permeability, compared with the wide-type lines after being cultivated for 5 days in 4°C. Gene expression and enzyme activities of the antioxidant system assay revealed the increased activities of SOD, CAT, MDHAR, and GR, and higher ASA/DHA ratio and GSH/GSSG ratio in transgenic lines. Additionally, overexpression of ABI4 also induced the expression of members of the Inducer of CBF expression genes (ICEs)-C-repeat binding transcription factor genes(CBFs)-Cold regulated genes (CORs) low-temperature response module. In summary, under low-temperature conditions, overexpression of ABI4 could enhance the content of endogenous ABA in plants through interactions with ABA2, which in turn reduced low-temperature damage in plants. This provides a new perspective for further understanding the molecular regulatory mechanism of plant response to low temperature and the improvement of plant cold tolerance.
4DRoot: Root phenotyping software for temporal 3D scans by X-ray computed tomography
Authors: Herrero-Huerta Monica , Raumonen Pasi , Gonzalez-Aguilera Diego
Published: September 2022

Currently, plant phenomics is considered the key to reducing the genotype-to-phenotype knowledge gap in plant breeding. In this context, breakthrough imaging technologies have demonstrated high accuracy and reliability. The X-ray computed tomography (CT) technology can noninvasively scan roots in 3D; however, it is urgently required to implement high-throughput phenotyping procedures and analyses to increase the amount of data to measure more complex root phenotypic traits. We have developed a spatial-temporal root architectural modeling software tool based on 4D data from temporal X-ray CT scans. Through a cylinder fitting, we automatically extract significant root architectural traits, distribution, and hierarchy. The open-source software tool is named 4DRoot and implemented in MATLAB. The source code is freely available at https://github.com/TIDOP-USAL/4DRoot. In this research, 3D root scans from the black walnut tree were analyzed, a punctual scan for the spatial study and a weekly time-slot series for the temporal one. 4DRoot provides breeders and root biologists an objective and useful tool to quantify carbon sequestration throw trait extraction. In addition, 4DRoot could help plant breeders to improve plants to meet the food, fuel, and fiber demands in the future, in order to increase crop yield while reducing farming inputs.
Disease diagnostic method based on cascade backbone network for apple leaf disease classification
Authors: Sheng Xing , Wang Fengyun , Ruan Huaijun , Fan Yangyang , Zheng Jiye , Zhang Yangyang , Lyu Chen
Published: September 2022

Fruit tree diseases are one of the major agricultural disasters in China. With the popularity of smartphones, there is a trend to use mobile devices to identify agricultural pests and diseases. In order to identify leaf diseases of apples more easily and efficiently, this paper proposes a cascade backbone network-based (CBNet) disease identification method to detect leaf diseases of apple trees in the field. The method first replaces traditional convolutional blocks with MobileViT-based convolutional blocks particularly for feature extraction. Compared with the traditional convolutional block, the MobileViT-based convolutional block is able to mine feature information in the image better. In order to refine the mined feature information, a feature refinement module is proposed in this paper. At the same time, this paper proposes a cascaded backbone network for effective fusion of features using a pyramidal cascaded multiplication operation. The results conducted on field datasets collected using mobile devices showed that the network proposed in this paper can achieve 96.76% accuracy and 96.71% F1-score. To the best of our knowledge, this paper is the first to introduce Transformer into apple leaf disease identification, and the results are promising.