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Summary: Structural variations (SVs) are major genetic variants that can be involved in the origin, adaptation and domestication of species. However, the identification and characterization of SVs in Spinacia species are rare due to the lack of a pan‐genome. Here, we report eight chromosome‐scale assemblies of cultivated spinach and its two wild species. After integration with five existing assemblies, we constructed a comprehensive Spinacia pan‐genome and identified 193 661 pan‐SVs, which were genotyped in 452 Spinacia accessions. Our pan‐SVs enabled genome‐wide association study identified signals associated with sex and clarified the evolutionary direction of spinach. Most sex‐linked SVs (86%) were biased to occur on the Y chromosome during the evolution of the sex‐linked region, resulting in reduced Y‐linked gene expression. The frequency of pan‐SVs among Spinacia accessions further illustrated the contribution of these SVs to domestication, such as bolting time and seed dormancy. Furthermore, compared with SNPs, pan‐SVs act as efficient variants in genomic selection (GS) because of their ability to capture missing heritability information and higher prediction accuracy. Overall, this study provides a valuable resource for spinach genomics and highlights the potential utility of pan‐SV in crop improvement and breeding programmes. [ABSTRACT FROM AUTHOR]

An in-depth understanding of gas (oxygen and methane) seepage characteristics in coal mine goafs is essential for the safe production of mines and for advancing sustainable development practices within the mining industry. However, the gas distribution and its flow processes still remain ambiguous. In this article, we developed a three-dimensional porous media mining goaf mathematical model (considering the heterogeneity) to analyze the methane and oxygen flow features. Firstly, based on the variation laws of the "three zones"—the free caving zone, fracture zone, and subsidence zone—porosity changes in the vertical direction were set. A three-dimensional physical model of a fully mechanized caving mining area with a "U"-shaped ventilation system was established as the basis, and a COMSOL Multiphysics multi-field coupled model was built. Secondly, based on the established model, the characteristics of porosity distribution, mixed gas pressure changes, and the volume fraction of oxygen in the goaf were analyzed. The results show that as the distance from the working face increases, the compaction intensity in the mined-out area gradually rises, resulting in a decreasing porosity trend. The porosity distribution characteristics significantly impact the mechanical behavior and gas flow. The gas pressure inside the mined-out area is much higher than the surroundings, decreasing with depth. The upper and middle parts have the highest-pressure concentrations, requiring focused assessment and targeted monitoring measures based on the pressure characteristics of different regions. The oxygen concentration gradually decreases with depth due to poor ventilation, leading to potential explosive gas mixtures, necessitating ventilation system optimization, enhanced monitoring, and emergency preparedness. The gas exhibits vertical stratification, with higher concentrations in the upper and deep regions. Targeted drainage and ventilation methods can effectively control the gas concentration and ensure production safety. [ABSTRACT FROM AUTHOR]

The old gob, as a potential CO2 geological storage reservoir, has huge storage potential. To clarify the distribution characteristics and storage capacity of CO2 in the old gob after different well deployment schemes, this study, based on the actual geological conditions of the old gob in the Huainan mining area, uses the COMSOL software to numerically simulate CO2 injection into the old gob, considering the heterogeneity of permeability and the difference in coal-rock adsorption capacity within the old gob. The research indicates that the distribution characteristics of CO2 are significantly influenced by the deployment scheme. Specifically, different deployment schemes result in varying CO2 concentrations and distribution patterns. Particularly, when the injection well is deployed at a depth of 65 m, the distribution of CO2 in the low-permeability upper part of the old gob will significantly increase and the horizontal distribution range will significantly decrease. Under different well deployment modes, the CO2 storage capacity varies significantly. When the injection well is deployed at a depth of 65 m, it is more conducive to the storage of CO2 than at other deeper depths and the total storage capacity is larger. In addition, increasing the number of monitoring wells helps the migration and diffusion of CO2 in the old gob. Reasonably increasing the number of monitoring wells and adopting a symmetric deployment mode can significantly improve the CO2 storage capacity in the old gob. Through a reasonable deployment scheme, the CO2 storage capacity in the old gob can be more than 1.8 times that of the single monitoring well deployment scheme. Overall, based on the analysis of the distribution characteristics and storage capacity, the vertical positioning of the injection wells and the deployment mode of the monitoring wells that are conducive to improving the CO2 storage capacity in the old gob are obtained, which can provide an important reference for the well deployment scheme of CO2 storage in the old gob. [ABSTRACT FROM AUTHOR]

Spinach (Spinacia oleracea L.) is commonly considered a dioecious plant with heterogametic (XY) and homogametic (XX) sex chromosomes. The characteristic is also utilized for the production of spinach hybrid seeds. However, the molecular mechanisms of sex determination in spinach are still unclear because of a lack of genomic and transcriptomic information. In this study, RNA sequencing (RNA-seq) was performed in male and female inflorescences to provide insight into the molecular basis of sex determination in spinach. Comparative transcriptome analyses showed that 2278 differentially expressed genes (DEGs) were identified between male and female inflorescences. A high correlation between the RNA-Seq and qRT-PCR validation for DEGs was observed. Among these, 182 DEGs were annotated to transcription factors including the MYB family protein, bHLH family, and MADS family, suggesting these factors might play a vital role in sex determination. Moreover, 26 DEGs related to flower development, including nine ABCE class genes, were detected. Expression analyses of hormone pathways showed that brassinosteroids may be key hormones related to sex determination in spinach. Overall, this study provides a large amount of DEGs related to sexual expression and lays a foundation for unraveling the regulatory mechanism of sex determination in spinach. Key words: spinach, dioecious, RNA-seq, floral sex determination, flower development. L'epinard (Spinacea oleraca L.) est generalement considere comme une plante dioique avec des chromosomes sexuels heterogametiques (XY) et homogametiques (XX). Cette caracteristique est egalement exploitee pour la production de semences hybrides chez l'epinard. Cependant, les mecanismes moleculaires de la determination du sexe demeurent nebuleux en raison de l'absence de donnees genomiques et transcriptomiques. Dans ce travail, une analyse RNA-seq a ete realisee sur les inflorescences males et femelles pour jeter un eclairage sur les assises moleculaires de la determination du sexe chez l'epinard. Des comparaisons des transcriptomes ont permis d'identifier 2278 genes exprimes de maniere differentielle (DEG) entre les inflorescences males et femelles. Une forte correlation a ete observee entre les donnees RNA-seq et des donnees de validation obtenues par qRT-PCR. Parmi les DEG, 182 sont annotes comme codant pour des facteurs de transcription dont certains sont de type MYB, bHLH et MADS, ce qui suggere que ces facteurs pourraient jouer des roles vitaux dans la determination du sexe. De plus, 26 DEG etaient associes au developpement floral, dont neuf genes de la classe ABCE. Des analyses de l'expression de sentiers hormonaux ont montre que les brassinosteroides seraient des hormones cles dans la determination du sexe chez l'epinard. Globalement, cette etude fournit un grand nombre de DEG presentant une expression differenciee selon le sexe et constitue une assise pour mieux comprendre les mecanismes regulant la determination du sexe chez l'epinard. [Traduit par la Redaction] Mots-cles: epinards, dioique, RNA-seq, determination du sexe des fleurs, developpement floral., Introduction The sexual system is remarkably complex in angiosperms. Monoecy and hermaphroditism are prevalent in angiosperms, while only a few species have evolved dioecy (Renner 2014). Hermaphroditic flowers have four [...]

Stem mustard, the main raw material for pickled mustard tuber, is widely planted in Chongqing, China, and is an important local cash crop. Under the working conditions of sticky and wet soil in the Chongqing area, conventional furrow seeding has problems such as soil sticking to the furrow opener, poor mulching effect, etc. In this regard, this paper proposes the use of non-contact, soil-based, pneumatic shot seeding, in which seeds are shot into the soil to a predetermined depth by a high-speed air stream. The diameter of stem mustard seeds was found to be 1.33 mm, with a spherical rate of 95.32% using physical and mechanical properties. The high-speed camera test was used to determine the air pressure at the appropriate sowing depth, and the seed entry process was simulated by EDEM 2021 software, which analysed the movement process of the seed after entering the soil, and the structure of the seeder was designed based on the resulting test data. The structural parameters of the shot seeding device were analysed by a hydrodynamic simulation using Fluent 2022 R1 software and the following results were obtained: an outlet pipe diameter DC of 2 mm, mixing zone length H of 10 mm, mixing zone inlet diameter D of 15 mm, and steady-state gas flow rate of 80 m/s. Simulation seeding verification was conducted on the final determined structural parameters of the seeding device, and the simulation results showed that the seed velocity could reach 32.3 m/s. In actual experiments, it was found that when the vertical velocity of the seeds was greater than or equal to 26.59 m/s, the seeds could be completely and stably seeded into the soil. Therefore, the designed seeding device can meet the conditions of actual seeding experiments. In conclusion, this research offers a practical guideline for the rapid and precise sowing of stem mustard. [ABSTRACT FROM AUTHOR]

The common bean (Phaseolus vulgaris L.) is an economically important food crop grown worldwide; however, its production is affected by various environmental stresses, including cold, heat, and drought stress. The plant U-box (PUB) protein family participates in various biological processes and stress responses, but the gene function and expression patterns of its members in the common bean remain unclear. Here, we systematically identified 63 U-box genes, including 8 tandem genes and 55 non-tandem genes, in the common bean. These PvPUB genes were unevenly distributed across 11 chromosomes, with chromosome 2 holding the most members of the PUB family, containing 10 PUB genes. The analysis of the phylogenetic tree classified the 63 PUB genes into three groups. Moreover, transcriptome analysis based on cold-tolerant and cold-sensitive varieties identified 4 differentially expressed PvPUB genes, suggesting their roles in cold tolerance. Taken together, this study serves as a valuable resource for exploring the functional aspects of the common bean U-box gene family and offers crucial theoretical support for the development of new cold-tolerant common bean varieties. [ABSTRACT FROM AUTHOR]

Spinach is a significant source of vitamins, minerals, and antioxidants. These nutrients make it delicious and beneficial for human health. However, the genetic mechanism underlying the accumulation of nutrients in spinach remains unclear. In this study, we analyzed the content of chlorophyll a, chlorophyll b, oxalate, nitrate, crude fiber, soluble sugars, manganese, copper, and iron in 62 different spinach accessions. Additionally, 3,356,182 high-quality, single-nucleotide polymorphisms were found using resequencing and used in a genome-wide association study. A total of 2077 loci were discovered that significantly correlated with the concentrations of the nutritional elements. Data mining identified key genes in these intervals for four traits: chlorophyll, oxalate, soluble sugar, and Fe. Our study provides insights into the genetic architecture of nutrient variation and facilitates spinach breeding for good nutrition. [ABSTRACT FROM AUTHOR]

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Bolting is a symbol of the transition from vegetative to reproductive growth in plants. Late bolting can effectively prolong the commercial value of spinach and is of great importance for spinach breeding. Bolting has complex regulatory networks, and current research on spinach bolting is relatively weak, with specific regulatory pathways and genes unclear. To clarify the regulatory characteristics and key genes related to bolting in spinach, we conducted a comparative transcriptome analysis. In this study, 18 samples from three periods of bolting-tolerant spinach material 12S3 and bolting-susceptible material 12S4 were analyzed using RNA-seq on, resulting in 10,693 differentially expressed genes (DEGs). Functional enrichment and co-expression trend analysis indicated that most DEGs were enriched in the photoperiod pathway, the hormone signaling pathway, and the cutin, suberin, and wax biosynthetic pathways. According to the weighted gene co-expression network analysis (WGCNA), SpFT (SOV4g003400), SOV4g040250, and SpGASA1 (SOV6g017600) were likely to regulate bolting through the gibberellin and photoperiod pathways, and SpELF4 (SOV1g028600) and SpPAT1 (SOV4g058860) caused differences in early and late bolting among different cultivars. These results provide important insights into the genetic control of bolting in spinach and will help elucidate the molecular mechanisms of bolting in leafy vegetables. [ABSTRACT FROM AUTHOR]