bluuebunny/crossref_metadata_2025 huggingface dataset:
Entinostat Improves Motor Function and Neuronal Damage Via Downregulating NLRP3 Inflammasome Activation After Spinal Cord Injury
Authors: Dai Chen , Liu Bin , Peng Bibo , Qu Bo , Lin Jiezhi , Peng Baogan , Li Duan-Ming
Published: December 2021

Background: Spinal cord injury (SCI), a major public health problem, has no effective treatment. A large number of studies have confirmed that histone deacetylases (HDACs) are involved in the physiologic processes that occur following SCI. We tried to uncover the potential neuroprotective role of entinostat (a class I HDAC inhibitor) in SCI.

Methods: We conducted a study on a preclinical mouse model of SCI and OGD-induced neuronal damage to present the role of entinostat by the analysis of motor function, histopathologic damage, local NLRP3 inflammasome activation, and neuronal damage.

Results: The results showed that entinostat suppressed HDAC activation (including HDAC1 and HDAC3 expression), improved the grip strength and BMS score, spinal edema, cell death, and local NLRP3 inflammasome activation in the spinal cord following SCI. Furthermore, entinostat significantly increased OGD-inhibited neuronal activity and decreased PI-positive cells, HDAC activation, caspase-1 activation, IL-1β and IL-18 levels, and NLRP3 expression.

Conclusion: In summary, we first documented that entinostat improved the motor function, histopathologic damage, and local inflammatory response and NLRP3 inflammasome activation in the spinal cord following SCI and also presented the neuroprotective role of OGD-induced neuronal damage via the NLRP3 inflammasome. Thus, our study has the potential to reveal the interaction between the HDAC and NLRP3 inflammasome in the pathologic process as well as SCI and further promote the clinical indications of HDACi entinostat and clinical treatment for the inflammatory response after SCI.
Intestinal Macrophage Autophagy and its Pharmacological Application in Inflammatory Bowel Disease
Authors: Zheng Yang , Yu Yang , Chen Xu-Feng , Yang Sheng-Lan , Tang Xiao-Long , Xiang Zheng-Guo
Published: November 2021

Inflammatory bowel disease (IBD), comprised of Crohn’s disease (CD) and ulcerative colitis (UC), is a group of chronic inflammatory disorders. IBD is regarded as a severe healthcare problem worldwide, with high morbidity and lethality. So far, despite of numerous studies on this issue, the specific mechanisms of IBD still remain unclarified and ideal treatments are not available for IBD. The intestinal mucosal barrier is vital for maintaining the function of the intestinal self-defensive system. Among all of the components, macrophage is an important one in the intestinal self-defensive system, normally protecting the gut against exotic invasion. However, the over-activation of macrophages in pathological conditions leads to the overwhelming induction of intestinal inflammatory and immune reaction, thus damaging the intestinal functions. Autophagy is an important catabolic mechanism. It has been proven to participate the regulation of various kinds of inflammation- and immune-related disorders via the regulation of inflammation in related cells. Here in this paper, we will review the role and mechanism of intestinal macrophage autophagy in IBD. In addition, several well-studied kinds of agents taking advantage of intestinal macrophage autophagy for the treatment of IBD will also be discussed. We aim to bring novel insights in the development of therapeutic strategies against IBD.
Narrow-Linewidth Laser Linewidth Measurement Technology
Authors: Bai Zhenxu , Zhao Zhongan , Qi Yaoyao , Ding Jie , Li Sensen , Yan Xiusheng , Wang Yulei , Lu Zhiwei
Published: November 2021

A narrow-linewidth laser with excellent temporal coherence is an important light source for microphysics, space detection, and high-precision measurement. An ultranarrow-linewidth output with a linewidth as narrow as subhertz has been generated with a theoretical coherence length over millions of kilometers. Traditional grating spectrum measurement technology has a wide wavelength scanning range and an extended dynamic range, but the spectral resolution can only reach the gigahertz level. The spectral resolution of a high-precision Fabry–Pérot interferometer can only reach the megahertz level. With the continuous improvement of laser coherence, the requirements for laser linewidth measurement technology are increasing, which also promotes the rapid development of narrow-linewidth lasers and their applications. In this article, narrow-linewidth measurement methods and their research progress are reviewed to provide a reference for researchers engaged in the development, measurement, and applications of narrow-linewidth lasers.
Skyrmion-Antiskyrmion Racetrack Memory in Rank-One DMI Materials
Authors: Hoffmann Markus , Müller Gideon P. , Melcher Christof , Blügel Stefan
Published: November 2021

Chiral magnetic skyrmions, localized and topologically protected vortex-like magnetic textures that can be found in chiral magnets, are currently under intense study as an entity for information storage and processing. A recent study showed that so-called rank-one materials can host both skyrmions and antiskyrmions at the same energy. In such systems the Dzyaloshinskii-Moriya interaction, in general a tensorial quantity, is reduced to only one non-zero component. The presence of both skyrmions and antiskyrmions allows for the investigation of the possible interplay between them. Here, we investigate the stability and interaction of skyrmions and antiskyrmions as well as their transport properties subject to spin-orbit torque for a model system described by an atomistic spin-lattice Hamiltonian employing the simulation software Spirit. The spin-orbit torque driven spin-dynamics described by the Landau-Lifshitz-Gilbert equation is compared to the effective one of the Thiele equation. We demonstrate that, even though skyrmions and antiskyrmions can be seen as antiparticles, a rather dense arrangement of both along a memory track is possible, enabling their use as representations of the binary data bits “0” and “1” in a memory device.
Risk Analysis of the Transmission Route for the African Swine Fever Virus in Mainland China
Authors: Hu Jiang-Hong , Pei Xin , Sun Gui-Quan , Jin Zhen
Published: November 2021

African swine fever first broke out in mainland China in August 2018 and has caused a substantial loss to China’s pig industry. Numerous investigations have confirmed that trades and movements of infected pigs and pork products, feeding pigs with contaminative swills, employees, and vehicles carrying the virus are the main transmission routes of the African swine fever virus (ASFV) in mainland China. However, which transmission route is more risky and what is the specific transmission map are still not clear enough. In this study, we crawl the data related to pig farms and slaughterhouses from Baidu Map by writing the Python language and then construct the pig transport network. Following this, we establish an ASFV transmission model over the network based on probabilistic discrete-time Markov chains. Furthermore, we propose spatiotemporal backward detection and forward transmission algorithms in semi-directed weighted networks. Through the simulation and calculation, the risk of transmission routes is analyzed, and the results reveal that the infection risk for employees and vehicles with the virus is the highest, followed by contaminative swills, and the transportation of pigs and pork products is the lowest; the most likely transmission map is deduced, and it is found that ASFV spreads from northeast China to southwest China and then to west; in addition, the infection risk in each province at different times is assessed, which can provide effective suggestions for the prevention and control of ASFV.
The Association Between Arterial Stiffness and Muscle Indices Among Healthy Subjects and Subjects With Cardiovascular Risk Factors: An Evidence-Based Review
Authors: Aminuddin Amilia , Noor Hashim Muhammad Fakhrurrazi , Mohd Zaberi Nur Aina Syazana , Zheng Wei Lee , Ching Chu Beh , Jamaludin Nur Amalina , Salamt Norizam , Che Roos Nur Aishah , Ugusman Azizah
Published: November 2021

Skeletal muscle is one of the major tissues in the body and is important for performing daily physical activity. Previous studies suggest that vascular dysfunction contributes to reduced skeletal muscle mass. However, the association between vascular dysfunction and muscle mass, muscle strength and muscle flexibility are less established. Therefore, the focus of this review was to investigate the association between arterial stiffness (AS) which is a marker of vascular function, and muscle indices among healthy and those with cardiovascular risk factors. Three databases were used to search for relevant studies. These keywords were used: “arterial stiffness” OR “vascular stiffness” OR “aortic stiffness” OR “pulse wave velocity” OR “carotid femoral pulse wave velocity” OR “pulse wave analysis” AND “muscle” OR “skeletal” OR “flexibility” OR “range of motion” OR “articular” OR “arthrometry” OR “strength” OR “hand strength” OR “pinch strength” OR “mass” OR “lean” OR “body composition.” The criteria were; (1) original, full-text articles, (2) articles written in English language, (3) human studies involving healthy adults and/or adults with cardiovascular disease (CVD) or CVD risk factors (4) articles that reported the relationship between AS (measured as carotid-femoral pulse wave velocity or brachial-ankle pulse wave velocity) and muscle indices (measured as muscle mass, muscle flexibility and muscle strength) after adjusting for relevant confounders. The search identified 2295 articles published between 1971 and June 2021. Only 17 articles fulfilled the criteria. Two studies showed an inverse association between AS and muscle strength in healthy subjects, whereas in subjects with CVD risk factors, five out of seven studies found an inverse correlation between the two parameters. Eleven studies showed an inverse association between AS and muscle mass in subjects with CVD and CVD risk factors. The association between AS and muscle flexibility was not studied in any of the articles reviewed. In conclusion, there is an inverse correlation between muscle indices and AS in healthy adults and those with CVD or CVD risk factors. However, most of the studies were cross-sectional studies, hence the need for future prospective studies to address this issue.
Dietary Observations of Ultra-Endurance Runners in Preparation for and During a Continuous 24-h Event
Authors: Kinrade Emma J. , Galloway Stuart D. R.
Published: November 2021

Carbohydrate (CHO) intake recommendations for events lasting longer than 3h indicate that athletes should ingest up to 90g.h.−1 of multiple transportable carbohydrates (MTC). We examined the dietary intake of amateur (males: n=11, females: n=7) ultra-endurance runners (mean age and mass 41.5±5.1years and 75.8±11.7kg) prior to, and during a 24-h ultra-endurance event. Heart rate and interstitial glucose concentration (indwelling sensor) were also tracked throughout the event. Pre-race diet (each 24 over 48h) was recorded via weighed intake and included the pre-race meal (1–4h pre-race). In-race diet (24h event) was recorded continuously, in-field, by the research team. Analysis revealed that runners did not meet the majority of CHO intake recommendations. CHO intake over 24–48h pre-race was lower than recommended (4.0±1.4g·kg−1; 42±9% of total energy), although pre-race meal CHO intake was within recommended levels (1.5±0.7g·kg−1). In-race CHO intake was only in the 30–60g·h−1 range (mean intake 33±12g·h−1) with suboptimal amounts of multiple transportable CHO consumed. Exercise intensity was low to moderate (mean 68%HRmax 45%VO2max) meaning that there would still be an absolute requirement for CHO to perform optimally in this ultra-event. Indeed, strong to moderate positive correlations were observed between distance covered and both CHO and energy intake in each of the three diet periods studied. Independent t-tests showed significantly different distances achieved by runners consuming ≥5 vs. <5g·kg−1 CHO in pre-race diet [98.5±18.7miles (158.5±30.1km) vs. 78.0±13.5miles (125.5±21.7km), p=0.04] and ≥40 vs. <40g·h−1 CHO in-race [92.2±13.9miles (148.4±22.4km) vs. 74.7±13.5miles (120.2±21.7km), p=0.02]. Pre-race CHO intake was positively associated with ultra-running experience, but no association was found between ultra-running experience and race distance. No association was observed between mean interstitial glucose and dietary intake, or with race distance. Further research should explore approaches to meeting pre-race dietary CHO intake as well as investigating strategies to boost in-race intake of multiple transportable CHO sources. In 24-h ultra-runners, studies examining the performance enhancing benefits of getting closer to meeting pre-race and in-race carbohydrate recommendations are required.
Acclimations to Cold and Warm Conditions Differently Affect the Energy Metabolism of Diapausing Larvae of the European Corn Borer Ostrinia nubilalis (Hbn.)
Authors: Popović Željko D. , Maier Vítězslav , Avramov Miloš , Uzelac Iva , Gošić-Dondo Snežana , Blagojević Duško , Koštál Vladimír
Published: November 2021

The European corn borer Ostrinia nubilalis is a pest species, whose fifth instar larvae gradually develop cold hardiness during diapause. The physiological changes underlying diapause progression and cold hardiness development are still insufficiently understood in insects. Here, we follow a complex of changes related to energy metabolism during cold acclimation (5°C) of diapausing larvae and compare this to warm-acclimated (22°C) and non-diapause controls. Capillary electrophoresis of nucleotides and coenzymes has shown that in gradually cold-acclimated groups concentrations of ATP/ADP and, consequently, energy charge slowly decrease during diapause, while the concentration of AMP increases, especially in the first months of diapause. Also, the activity of cytochrome c oxidase (COX), as well as the concentrations of NAD+ and GMP, decline in cold-acclimated groups, until the latter part of diapause, when they recover. Relative expression of NADH dehydrogenase (nd1), coenzyme Q-cytochrome c reductase (uqcr), COX, ATP synthase (atp), ADP/ATP translocase (ant), and prohibitin 2 (phb2) is supressed in cold-acclimated larvae during the first months of diapause and gradually increases toward the termination of diapause. Contrary to this, NADP+ and UMP levels significantly increased in the first few months of diapause, after gradual cold acclimation, which is in connection with the biosynthesis of cryoprotective molecules, as well as regeneration of small antioxidants. Our findings evidence the existence of a cold-induced energy-saving program that facilitates long-term maintenance of larval diapause, as well as gradual development of cold hardiness. In contrast, warm acclimation induced faster depletion of ATP, ADP, UMP, NAD+, and NADP+, as well as higher activity of COX and generally higher expression of all energy-related genes in comparison to cold-acclimated larvae. Moreover, such unusually high metabolic activity, driven by high temperatures, lead to premature mortality in the warm-acclimated group after 2 months of diapause. Thus, our findings strongly support the importance of low temperature exposure in early diapause for gradual cold hardiness acquisition, successful maintenance of the resting state and return to active development. Moreover, they demonstrate potentially adverse effects of global climate changes and subsequent increase in winter temperatures on cold-adapted terrestrial organisms in temperate and subpolar regions.
Effects of Herbal Adaptogen Feed-Additive on Growth Performance, Carcass Parameters, and Muscle Amino Acid Profile in Heat-Stressed Modern Broilers
Authors: Greene Elizabeth S. , Maynard Clay , Owens Casey M. , Meullenet Jean-François , Dridi Sami
Published: November 2021

Heat stress has strong adverse effects on poultry production and, thereby, threats its sustainability, which energized scientists to search for innovative and effective solutions. Here, we undertook this study to evaluate the effects of in-feed herbal adaptogen (stress response modifier) supplementation on growth performances, meat quality, and breast amino acid profile in chronic cyclic heat-stressed broilers. Day-old male Cobb 500 chicks (n = 720) were randomly assigned, in environmental chambers (n = 12, 24 pens), to three diet-treatments: a three-phase corn-soybean based diet fed as such (Control, C), or supplemented with the herbal adaptogen at 500 g/1000 kg control diet (NR-PHY-500) or at 1 kg/1000 kg control diet (NR-PHY-1000). From d29 to d42, birds from 9 chambers were exposed to cyclic heat stress (HS, 35°C from 9:30 am-5:30 pm), however, the rest of the chamber were maintained at thermoneutral conditions (24°C, TN), which creates 4 experimental groups: C-TN, C-HS, NR-PHY-500HS, and NR-PHY-1000HS (6 pens/group, 168 birds/group). HS altered growth performance via depression of feed intake and body weight. Adaptogen supplementation stimulated feed intake and averaged 65.95 and 83.25 g better body weight and 5 and 10 points better FCR at low and high dose, respectively, compared to heat-stressed birds. This increase in body weight was mirrored in enhanced weights of body parts (breast, tender, wings, and legs). Adaptogen supplementation modulated also breast amino acid profile, pH, color, and quality. Together, these data suggested that adaptogen supplementation could be a promising solution to alleviate heat stress, however further in-depth investigation for its mode of action and its underlying mechanisms are warranted.
Effects of Pre-, Post- and Intra-Exercise Hyperbaric Oxygen Therapy on Performance and Recovery: A Systematic Review and Meta-Analysis
Authors: Huang Xizhang , Wang Ran , Zhang Zheng , Wang Gang , Gao Binghong
Published: November 2021

Background: As a World Anti-doping Agency (WADA)-approved treatment, hyperbaric oxygen (HBO2) therapy has been used to improve exercise performance in sports practice.

Objective: We aimed to investigate the effect of pre-, post-, and intra-exercise HBO2 therapy on performance and recovery.

Methods: A literature search was conducted using EMBASE, CENTRAL, PubMed, Web of Science, and SPORTDiscus to obtain literature published until May 2021. A total of 1,712 studies that met the following criteria were identified: (1) enrolled healthy adults who were considered physically active; (2) evaluated HBO2 therapy; (3) included a control group exposed to normobaric normoxic (NN) conditions; (4) involved physical testing (isokinetic or dynamic strength exercise, maximal incremental treadmill/cycle exercise, etc.); and (5) included at least one exercise performance/recovery index as an outcome measure. The Cochrane risk of bias assessment tool was used to evaluate the included studies, and the heterogeneity of therapy effects was assessed using the I2 statistic by Review Manager 5.3.

Results: Ten studies (166 participants) were included in the qualitative analysis, and six studies (69 participants) were included in the quantitative synthesis (meta-analysis). In comparisons between participants who underwent HBO2 therapy and NN conditions, the effects of pre-exercise HBO2 therapy on exercise performance were not statistically significant (P > 0.05), and the effects of post-exercise HBO2 therapy on recovery were not statistically significant either (P > 0.05). Although individual studies showed positive effects of intra-exercise HBO2 therapy on exercise performance, a meta-analysis could not be performed.

Conclusion: Hyperbaric oxygen therapy before or after exercise had no significant effect on performance and recovery. However, hyperbaric oxygen therapy during exercise could improve muscle endurance performance, which needs to be confirmed by further empirical studies. At present, the practical relevance of these findings should be treated with caution.
lepidium-like, a Naturally Occurring Mutant of Capsella bursa-pastoris, and Its Implications on the Evolution of Petal Loss in Cruciferae
Authors: Klepikova Anna V. , Shnayder Elina D. , Kasianov Artem S. , Remizowa Margarita V. , Sokoloff Dmitry D. , Penin Aleksey A.
Published: December 2021

Naturally occurring mutants whose phenotype recapitulates the changes that distinguish closely related species are of special interest from the evolutionary point of view. They can give a key about the genetic control of the changes that led to speciation. In this study, we described lepidium-like (lel), a naturally occurring variety of an allotetraploid species Capsella bursa-pastoris that is characterized by the typical loss of all four petals. In some cases, one or two basal flowers in the raceme had one or two small petals. The number and structure of other floral organs are not affected. Our study of flower development in the mutant showed that once initiated, petals either cease further development and cannot be traced in anthetic flowers or sometimes develop to various degrees. lel plants showed an earlier beginning of floral organ initiation and delayed petal initiation compared to the wild-type plants. lel phenotype has a wide geographical distribution, being found at the northern extremity of the species range as well as in the central part. The genetic analysis of inheritance demonstrated that lel phenotype is controlled by two independent loci. While the flower in the family Cruciferae generally has a very stable structure (i.e., four sepals, four petals, six stamens, and two carpels), several deviations from this ground plan are known, in particular in the genus Lepidium, C. bursa-pastoris is an emerging model for the study of polyploidy (which is also very widespread in Cruciferae); the identification and characterization of the apetalous mutant lays a foundation for further research of morphological evolution in polyploids.
Transcriptomic Characterization of the Effects of Selenium on Maize Seedling Growth
Authors: Dou Lingling , Tian Zailong , Zhao Qin , Xu Mengting , Zhu Yiran , Luo Xiaoyue , Qiao Xinxing , Ren Rui , Zhang Xianliang , Li Huaizhu
Published: November 2021

Selenium (Se) is a trace mineral element in soils that can be beneficial to plants in small amounts. Although maize is among the most economically important crops, there are few reports on the effects of Se on maize seedling growth at the molecular level. In this study, the growth of maize seedlings treated with different concentrations of Na2SeO3 was investigated, and the physiological characteristics were measured. Compared with the control, a low Se concentration promoted seedling growth, whereas a high Se concentration inhibited it. To illustrate the transcriptional effects of Se on maize seedling growth, samples from control plants and those treated with low or high concentrations of Se were subjected to RNA sequencing. The differentially expressed gene (DEG) analysis revealed that there were 239 upregulated and 106 downregulated genes in the low Se treatment groups, while there were 845 upregulated and 1,686 downregulated DEGs in the high Se treatment groups. Both the Gene Ontology (GO) and the Kyoto Encyclopedia of Genes and Genomes (KEGG) annotation analyses showed a low concentration of the Se-stimulated expression of “DNA replication” and “glutathione (GSH) metabolism”-related genes. A high concentration of Se repressed the expression of auxin signal transduction and lignin biosynthesis-related genes. The real-time quantitative reverse transcription PCR (qRT-PCR) results showed that in the low Se treatment, “auxin signal transduction,” “DNA replication,” and lignin biosynthesis-related genes were upregulated 1.4- to 57.68-fold compared to the control, while, in the high Se concentration treatment, auxin signal transduction and lignin biosynthesis-related genes were downregulated 1.6- to 16.23-fold compared to the control. Based on these transcriptional differences and qRT-PCR validation, it was found that a low dosage of Se may promote maize seedling growth but becomes inhibitory to growth at higher concentrations. This study lays a foundation for the mechanisms underlying the effects of Se on maize seedling growth.
Recombinase Polymerase Amplification/Cas12a-Based Identification of Xanthomonas arboricola pv. pruni on Peach
Authors: Luo Mei , Meng Fan-Zhu , Tan Qin , Yin Wei-Xiao , Luo Chao-Xi
Published: November 2021

Peach bacterial spot caused by Xanthomonas arboricola pv. pruni (Xap) is a devastating disease worldwide and frequently causes massive economic losses. In recent years, it has become a pandemic outbreak in most peach production areas of China, especially on precocious peaches in the middle reach of the Yangtze River. Rapid, user-friendly detection is extremely important to make the correct diagnosis and develop suitable control strategies. In this study, we described a recombinase polymerase amplification (RPA)/Cas12a-based system that combines RPA and CRISPR/Cas12a for Xap identification. A total of three crRNAs were designed to target a highly conserved ABC transporter ATP-binding protein-encoding gene ftsX to make specific detection of Xap. Results showed that crRNA 2 and crRNA 3 could get consistent detection for Xap. To realize the visualization of detection results, we additionally introduced FQ-reporter and FB-reporter. The developed method was highly sensitive and could detect as low as 10–18 M Xap gDNA with a mini-UV torch, corresponding to 1.63 copies/μl or 8.855 fg/μl gDNA of Xap, while with lateral flow strips, the sensitivity was 10–17 M. In addition, this method could specifically detect Xap from other closely related bacteria or pathogens associated with peach diseases. Furthermore, this method could make correct identification for Xap with crude DNA using NaOH-based extraction (3 min) directly from diseased peach samples. Considering that the developed method could get results within 2 h and could be performed at 37°C (body temperature), it is promising to be applied for Xap diagnosis and monitoring in fields.
Estimating Leaf Area Index in Row Crops Using Wheel-Based and Airborne Discrete Return Light Detection and Ranging Data
Authors: Nazeri Behrokh , Crawford Melba M. , Tuinstra Mitchell R.
Published: December 2021

Leaf area index (LAI) is an important variable for characterizing plant canopy in crop models. It is traditionally defined as the total one-sided leaf area per unit ground area and is estimated by both direct and indirect methods. This paper explores the effectiveness of using light detection and ranging (LiDAR) data to estimate LAI for sorghum and maize with different treatments at multiple times during the growing season from both a wheeled vehicle and Unmanned Aerial Vehicles. Linear and nonlinear regression models are investigated for prediction utilizing statistical and plant structure-based features extracted from the LiDAR point cloud data with ground reference obtained from an in-field plant canopy analyzer (indirect method). Results based on the value of the coefficient of determination (R2) and root mean squared error for predictive models ranged from ∼0.4 in the early season to ∼0.6 for sorghum and ∼0.5 to 0.80 for maize from 40 Days after Sowing to harvest.
Continuous Mapping Identifies Loci Associated With Weevil Resistance [Cosmopolites sordidus (Germar)] in a Triploid Banana Population
Authors: Uwimana Brigitte , Mwanje Gerald , Batte Michael , Akech Violet , Shah Trushar , Vuylsteke Marnik , Swennen Rony
Published: December 2021

The first step toward marker-assisted selection is linking the phenotypes to molecular markers through quantitative trait loci (QTL) analysis. While the process is straightforward in self-pollinating diploid (2x) species, QTL analysis in polyploids requires unconventional methods. In this study, we have identified markers associated with weevil Cosmopolites sordidus (Germar) resistance in bananas using 138 triploid (2n = 3x) hybrids derived from a cross between a tetraploid “Monyet” (2n = 4x) and a 2x “Kokopo” (2n = 2x) banana genotypes. The population was genotyped by Diversity Arrays Technology Sequencing (DArTSeq), resulting in 18,009 polymorphic single nucleotide polymorphisms (SNPs) between the two parents. Marker–trait association was carried out by continuous mapping where the adjusted trait means for the corm peripheral damage (PD) and total cross-section damage (TXD), both on the logit scale, were regressed on the marker allele frequencies. Forty-four SNPs that were associated with corm PD were identified on the chromosomes 5, 6, and 8, with 41 of them located on chromosome 6 and segregated in “Kokopo.” Eleven SNPs associated with corm total TXD were identified on chromosome 6 and segregated in “Monyet.” The additive effect of replacing one reference allele with the alternative allele was determined at each marker position. The PD QTL was confirmed using conventional QTL linkage analysis in the simplex markers segregating in “Kokopo” (AAAA × RA). We also identified 43 putative genes in the vicinity of the markers significantly associated with the two traits. The identified loci associated with resistance to weevil damage will be used in the efforts of developing molecular tools for marker-assisted breeding in bananas.
Accelerating Adaptation of Forest Trees to Climate Change Using Individual Tree Response Functions
Authors: Poupon Valérie , Chakraborty Debojyoti , Stejskal Jan , Konrad Heino , Schueler Silvio , Lstibůrek Milan
Published: November 2021

In forest tree breeding, assisted migration has been proposed to accelerate the adaptive response to climate change. Response functions are currently fitted across multiple populations and environments, enabling selections of the most appropriate seed sources for a specific reforestation site. So far, the approach has been limited to capturing adaptive variation among populations, neglecting tree-to-tree variation residing within a population. Here, we combined the response function methodology with the in-situ breeding approach, utilizing progeny trials of European larch (Larix decidua) across 21 test sites in Austria ranging from Alpine to lowland regions. We quantified intra-population genetic variance and predicted individual genetic performance along a climatic gradient. This approach can be adopted in most breeding and conservation programs, boosting the speed of adaptation under climate change.
QTL Analysis of Five Silique-Related Traits in Brassica napus L. Across Multiple Environments
Authors: Zhao Xiaozhen , Yu Kunjiang , Pang Chengke , Wu Xu , Shi Rui , Sun Chengming , Zhang Wei , Chen Feng , Zhang Jiefu , Wang Xiaodong
Published: November 2021

As an important physiological and reproductive organ, the silique is a determining factor of seed yield and a breeding target trait in rapeseed (Brassica napus L.). Genetic studies of silique-related traits are helpful for rapeseed marker-assisted high-yield breeding. In this study, a recombinant inbred population containing 189 lines was used to perform a quantitative trait loci (QTLs) analysis for five silique-related traits in seven different environments. As a result, 120 consensus QTLs related to five silique-related traits were identified, including 23 for silique length, 25 for silique breadth, 29 for silique thickness, 22 for seed number per silique and 21 for silique volume, which covered all the chromosomes, except C5. Among them, 13 consensus QTLs, one, five, two, four and one for silique length, silique breadth, silique thickness, seed number per silique and silique volume, respectively, were repeatedly detected in multiple environments and explained 4.38–13.0% of the phenotypic variation. On the basis of the functional annotations of Arabidopsis homologous genes and previously reported silique-related genes, 12 potential candidate genes underlying these 13 QTLs were screened and found to be stable in multiple environments by analyzing the re-sequencing results of the two parental lines. These findings provide new insights into the gene networks affecting silique-related traits at the QTL level in rapeseed.
Tapetal 3-Ketoacyl-Coenzyme A Synthases Are Involved in Pollen Coat Lipid Accumulation for Pollen-Stigma Interaction in Arabidopsis
Authors: Zhang Zaibao , Zhan Huadong , Lu Jieyang , Xiong Shuangxi , Yang Naiying , Yuan Hongyu , Yang Zhong-Nan
Published: November 2021

Pollen coat lipids form an outer barrier to protect pollen itself and play essential roles in pollen-stigma interaction. However, the precise molecular mechanisms underlying the production, deposition, regulation, and function of pollen coat lipids during anther development remain largely elusive. In lipid metabolism, 3-ketoacyl-coenzyme A synthases (KCS) are involved in fatty acid elongation or very-long-chain fatty acid (VLCFA) synthesis. In this study, we identified six members of the Arabidopsis KCS family expressed in anther. Among them, KCS7, KCS15, and KCS21 were expressed in tapetal cells at anther stages 8–10. Further analysis demonstrated that they act downstream of male sterility 1 (MS1), a regulator of late tapetum development. The kcs7/15/21 triple mutant is fertile. Both cellular observation and lipid staining showed pollen coat lipid was decreased in kcs7/15/21 triple mutant. After landing on stigma, the wild-type pollen grains were hydrated for about 5 min while the kcs7/15/21 triple mutant pollen took about 10 min to hydrate. Pollen tube growth of the triple mutant was also delayed. These results demonstrate that the tapetum-localized KCS proteins are involved in the accumulation of pollen coat lipid and reveal the roles of tapetal-derived pollen coat lipid for pollen-stigma interaction.
Phospholipase Dα1 Acts as a Negative Regulator of High Mg2+-Induced Leaf Senescence in Arabidopsis
Authors: Kocourková Daniela , Kroumanová Kristýna , Podmanická Tereza , Daněk Michal , Martinec Jan
Published: December 2021

Magnesium (Mg2+) is a macronutrient involved in essential cellular processes. Its deficiency or excess is a stress factor for plants, seriously affecting their growth and development and therefore, its accurate regulation is essential. Recently, we discovered that phospholipase Dα1 (PLDα1) activity is vital in the stress response to high-magnesium conditions in Arabidopsis roots. This study shows that PLDα1 acts as a negative regulator of high-Mg2+-induced leaf senescence in Arabidopsis. The level of phosphatidic acid produced by PLDα1 and the amount of PLDα1 in the leaves increase in plants treated with high Mg2+. A knockout mutant of PLDα1 (pldα1-1), exhibits premature leaf senescence under high-Mg2+ conditions. In pldα1-1 plants, higher accumulation of abscisic and jasmonic acid (JA) and impaired magnesium, potassium and phosphate homeostasis were observed under high-Mg2+ conditions. High Mg2+ also led to an increase of starch and proline content in Arabidopsis plants. While the starch content was higher in pldα1-1 plants, proline content was significantly lower in pldα1-1 compared with wild type plants. Our results show that PLDα1 is essential for Arabidopsis plants to cope with the pleiotropic effects of high-Mg2+ stress and delay the leaf senescence.
Genetic Architecture of Novel Sources for Reproductive Cold Tolerance in Sorghum
Authors: Chakrabarty Subhadra , Kravcov Natalja , Schaffasz André , Snowdon Rod J. , Wittkop Benjamin , Windpassinger Steffen
Published: November 2021

Enhancements in reproductive cold tolerance of sorghum are essential to expand growing areas into both high-latitude temperate areas and tropical high-altitude environments. Here we present first insights into the genetic architecture of this trait via genome-wide association studies in a broad genetic diversity set (n = 330) phenotyped in multi-location field trials including high-altitude tropical (Mexico) and high-latitude temperate (Germany) environments. We observed a high degree of phenotypic variation and identified several novel, temperate-adapted accessions with superior and environmentally stable cold tolerance. Good heritability indicates strong potential for implementation of reproductive cold tolerance in breeding. Although the trait was found to be strongly quantitative, promising genomic regions with multiple-trait associations were found, including hotspots on chromosomes 3 and 10 which contain candidate genes implicated in different developmental and survival processes under abiotic stress conditions.
Chromosome-Scale Genome Assembly for Chinese Sour Jujube and Insights Into Its Genome Evolution and Domestication Signature
Authors: Shen Lian-Ying , Luo Hang , Wang Xiao-Ling , Wang Xue-Meng , Qiu Xiao-Jing , Liu Hui , Zhou Shan-Shan , Jia Kai-Hua , Nie Shuai , Bao Yu-Tao , Zhang Ren-Gang , Yun Quan-Zheng , Chai Ying-Hui , Lu Jin-Ying , Li Yu , Zhao Shu-Wei , Mao Jian-Feng , Jia Shan-Gang , Mao Yong-Min
Published: November 2021

Sour or wild jujube fruits and dried seeds are popular food all over the world. In this study, we reported a high-quality genome assembly of sour jujube (Ziziphus jujuba Mill. var. spinosa), with a size of 406 Mbp and scaffold N50 of 30.3 Mbp, which experienced only γ hexaploidization event, without recent genome duplication. Population structure analysis identified four jujube subgroups (two domesticated ones, i.e., D1 in West China and D2 in East/SouthEast China, semi-wild, and wild), which underwent an evolutionary history of a significant decline of effective population size during the Last Glacial Period. The respective selection signatures of three subgroups were discovered, such as strong peaks on chromosomes #3 in D1, #1 in D2, and #4 in wild. Genes under the most significant selection on chromosomes #4 in wild were confirmed to be involved in fruit variations among jujube accessions, in transcriptomic analysis. Our study offered novel insights into the jujube population structure and domestication and provided valuable genomic resources for jujube improvement in stress response and fruit flavor in the future.
Integrative Morphological, Physiological, Proteomics Analyses of Jujube Fruit Development Provide Insights Into Fruit Quality Domestication From Wild Jujube to Cultivated Jujube
Authors: Huang Jian , Chen Xin , He Aobing , Ma Zhibo , Gong Tianqi , Xu Kenong , Chen Ruihong
Published: November 2021

Jujube (Ziziphus jujuba) was domesticated from wild jujube (Z. jujuba var. spinosa). Here, integrative physiological, metabolomic, and comparative proteomic analyses were performed to investigate the fruit expansion and fruit taste components in a jujube cultivar ‘Junzao’ and a wild jujube ‘Qingjiansuanzao’ with contrasting fruit size and taste. We revealed that the duration of cell division and expansion largely determined the final fruit size, while the intercellular space in the mesocarp dictated the ratio of mesocarp volume in mature fruits. The high levels of endogenous gibbereline3 (GA) and zeatin in the growing fruit of ‘Junzao’ were associated with their increased fruit expansion. Compared with ‘Junzao,’ wild jujube accumulated lower sugars and higher organic acids. Furthermore, several protein co-expression modules and important member proteins correlated with fruit expansion, sugar synthesis, and ascorbic acid metabolism were identified. Among them, GA20OX involved in GA biosynthesis was identified as a key protein regulating fruit expansion, whereas sucrose-6-phosphate synthase (SPS) and neutral invertase (NINV) were considered as key enzymes promoting sugar accumulation and as major factors regulating the ratio of sucrose to hexose in jujube fruits, respectively. Moreover, the increase of Nicotinamide adenine dinucleotide-Malate dehydrogenase (NAD-MDH) activity and protein abundance were associated with the malic acid accumulation, and the high accumulation of ascorbic acid in wild jujube was correlated with the elevated abundance of GalDH, ZjAPXs, and MDHAR1, which are involved in the ascorbic acid biosynthesis and recycling pathways. Overall, these results deepened the understanding of mechanisms regulating fruit expansion and sugar/acids metabolisms in jujube fruit.
Genetic Dissection of Hybrid Performance and Heterosis for Yield-Related Traits in Maize
Authors: Li Dongdong , Zhou Zhiqiang , Lu Xiaohuan , Jiang Yong , Li Guoliang , Li Junhui , Wang Haoying , Chen Shaojiang , Li Xinhai , Würschum Tobias , Reif Jochen C. , Xu Shizhong , Li Mingshun , Liu Wenxin
Published: December 2021

Heterosis contributes a big proportion to hybrid performance in maize, especially for grain yield. It is attractive to explore the underlying genetic architecture of hybrid performance and heterosis. Considering its complexity, different from former mapping method, we developed a series of linear mixed models incorporating multiple polygenic covariance structures to quantify the contribution of each genetic component (additive, dominance, additive-by-additive, additive-by-dominance, and dominance-by-dominance) to hybrid performance and midparent heterosis variation and to identify significant additive and non-additive (dominance and epistatic) quantitative trait loci (QTL). Here, we developed a North Carolina II population by crossing 339 recombinant inbred lines with two elite lines (Chang7-2 and Mo17), resulting in two populations of hybrids signed as Chang7-2 × recombinant inbred lines and Mo17 × recombinant inbred lines, respectively. The results of a path analysis showed that kernel number per row and hundred grain weight contributed the most to the variation of grain yield. The heritability of midparent heterosis for 10 investigated traits ranged from 0.27 to 0.81. For the 10 traits, 21 main (additive and dominance) QTL for hybrid performance and 17 dominance QTL for midparent heterosis were identified in the pooled hybrid populations with two overlapping QTL. Several of the identified QTL showed pleiotropic effects. Significant epistatic QTL were also identified and were shown to play an important role in ear height variation. Genomic selection was used to assess the influence of QTL on prediction accuracy and to explore the strategy of heterosis utilization in maize breeding. Results showed that treating significant single nucleotide polymorphisms as fixed effects in the linear mixed model could improve the prediction accuracy under prediction schemes 2 and 3. In conclusion, the different analyses all substantiated the different genetic architecture of hybrid performance and midparent heterosis in maize. Dominance contributes the highest proportion to heterosis, especially for grain yield, however, epistasis contributes the highest proportion to hybrid performance of grain yield.
Water Deficit Modulates the CO2 Fertilization Effect on Plant Gas Exchange and Leaf-Level Water Use Efficiency: A Meta-Analysis
Authors: Li Fei , Guo Dagang , Gao Xiaodong , Zhao Xining
Published: December 2021

Elevated atmospheric CO2 concentrations ([eCO2]) and soil water deficits significantly influence gas exchange in plant leaves, affecting the carbon-water cycle in terrestrial ecosystems. However, it remains unclear how the soil water deficit modulates the plant CO2 fertilization effect, especially for gas exchange and leaf-level water use efficiency (WUE). Here, we synthesized a comprehensive dataset including 554 observations from 54 individual studies and quantified the responses for leaf gas exchange induced by e[CO2] under water deficit. Moreover, we investigated the contribution of plant net photosynthesis rate (Pn) and transpiration rates (Tr) toward WUE in water deficit conditions and e[CO2] using graphical vector analysis (GVA). In summary, e[CO2] significantly increased Pn and WUE by 11.9 and 29.3% under well-watered conditions, respectively, whereas the interaction of water deficit and e[CO2] slightly decreased Pn by 8.3%. Plants grown under light in an open environment were stimulated to a greater degree compared with plants grown under a lamp in a closed environment. Meanwhile, water deficit reduced Pn by 40.5 and 37.8%, while increasing WUE by 24.5 and 21.5% under ambient CO2 concentration (a[CO2]) and e[CO2], respectively. The e[CO2]-induced stimulation of WUE was attributed to the common effect of Pn and Tr, whereas a water deficit induced increase in WUE was linked to the decrease in Tr. These results suggested that water deficit lowered the stimulation of e[CO2] induced in plants. Therefore, fumigation conditions that closely mimic field conditions and multi-factorial experiments such as water availability are needed to predict the response of plants to future climate change.
Genome-Wide Association Studies of Soybean Yield-Related Hyperspectral Reflectance Bands Using Machine Learning-Mediated Data Integration Methods
Authors: Yoosefzadeh-Najafabadi Mohsen , Torabi Sepideh , Tulpan Dan , Rajcan Istvan , Eskandari Milad
Published: November 2021

In conjunction with big data analysis methods, plant omics technologies have provided scientists with cost-effective and promising tools for discovering genetic architectures of complex agronomic traits using large breeding populations. In recent years, there has been significant progress in plant phenomics and genomics approaches for generating reliable large datasets. However, selecting an appropriate data integration and analysis method to improve the efficiency of phenome-phenome and phenome-genome association studies is still a bottleneck. This study proposes a hyperspectral wide association study (HypWAS) approach as a phenome-phenome association analysis through a hierarchical data integration strategy to estimate the prediction power of hyperspectral reflectance bands in predicting soybean seed yield. Using HypWAS, five important hyperspectral reflectance bands in visible, red-edge, and near-infrared regions were identified significantly associated with seed yield. The phenome-genome association analysis of each tested hyperspectral reflectance band was performed using two conventional genome-wide association studies (GWAS) methods and a machine learning mediated GWAS based on the support vector regression (SVR) method. Using SVR-mediated GWAS, more relevant QTL with the physiological background of the tested hyperspectral reflectance bands were detected, supported by the functional annotation of candidate gene analyses. The results of this study have indicated the advantages of using hierarchical data integration strategy and advanced mathematical methods coupled with phenome-phenome and phenome-genome association analyses for a better understanding of the biology and genetic backgrounds of hyperspectral reflectance bands affecting soybean yield formation. The identified yield-related hyperspectral reflectance bands using HypWAS can be used as indirect selection criteria for selecting superior genotypes with improved yield genetic gains in large breeding populations.