Volatile Profile Characterization of Jujube Fruit via HS-SPME-GC/MS and Sensory Evaluation.

Current research does not fully elucidate the key compounds and their mechanisms that define the aroma profile of fresh jujube fruits. Therefore, this study conducted a comprehensive analysis of both free and glycosidically bound aroma compounds in fresh jujube fruits of ten cultivars. Utilizing gas chromatography-mass spectrometry (GC-MS), we identified 76 volatile free aroma compounds and 19 glycosidically bound volatile compounds, with esters, aldehydes, and ketones emerging as the predominant volatile compounds in the jujube fruits. Odor activity value (OAV) analysis revealed that the primary aroma profile of the jujubes is characterized by fruity and fatty odors, with ß-damascenone being a key contributor to the fruity aroma, and (E)-2-oct-en-1-al and nonanal significantly influencing the fatty aroma. Moreover, the integration of sensory evaluation and partial least squares regression (PLSR) analysis pinpointed octanal, (E)-2-oct-en-1-al, nonanal, ß-damascenone, and pentanal as significant contributors to the jujube's characteristic aroma, while isoamyl acetate was identified as significantly influencing the fatty acid taste. This study not only underscores the complexity of the jujube aroma composition but also highlights the impact of environmental factors on aroma profiles, offering valuable insights into the sensory characteristics of jujube fruits.

Identification of Key Genes of Fruit Shape Variation in Jujube with Integrating Elliptic Fourier Descriptors and Transcriptome.

Jujube (Ziziphus jujuba) exhibits a rich diversity in fruit shape, with natural occurrences of gourd-like, flattened, and other special shapes. Despite the ongoing research into fruit shape, studies integrating elliptical Fourier descriptors (EFDs) with both Short Time-series Expression Miner (STEM) and weighted gene co-expression network analysis (WGCNA) for gene discovery remain scarce. In this study, six cultivars of jujube fruits with distinct shapes were selected, and samples were collected from the fruit set period to the white mature stage across five time points for shape analysis and transcriptome studies. By combining EFDs with WGCNA and STEM, the study aimed to identify the critical periods and key genes involved in the formation of jujube fruit shape. The findings indicated that the D25 (25 days after flowering) is crucial for the development of jujube fruit shape. Moreover, ZjAGL80, ZjABI3, and eight other genes have been implicated to regulate the shape development of jujubes at different periods of fruit development, through seed development and fruit development pathway. In this research, EFDs were employed to precisely delineate the shape of jujube fruits. This approach, in conjunction with transcriptome, enhanced the precision of gene identification, and offered an innovative methodology for fruit shape analysis. This integration facilitates the advancement of research into the morphological characteristics of plant fruits, underpinning the development of a refined framework for the genetic underpinnings of fruit shape variation.

Transcriptome profiles reveal response mechanisms and key role of PsNAC1 in Pinus sylvestris var. mongolica to drought stress.

BACKGROUND: Drought stress severely impedes plant growth, and only a limited number of species exhibit long-term resistance to such conditions. Pinus sylvestris var. mongolica, a dominant tree species in arid and semi-arid regions of China, exhibits strong drought resistance and plays a crucial role in the local ecosystem. However, the molecular mechanisms underlying this resistance remain poorly understood. RESULTS: Here, we conducted transcriptome sequence and physiological indicators analysis of needle samples during drought treatment and rehydration stages. De-novo assembly yielded approximately 114,152 unigenes with an N50 length of 1,363 bp. We identified 6,506 differentially expressed genes (DEGs), with the majority being concentrated in the heavy drought stage (4,529 DEGs). Functional annotation revealed enrichment of drought-related GO terms such as response to water (GO:0009415: enriched 108 genes) and response to water deprivation (GO:0009414: enriched 106 genes), as well as KEGG categories including MAPK signaling pathway (K04733: enriched 35 genes) and monoterpenoid biosynthesis (K21374: enriched 27 genes). Multiple transcription factor families and functional protein families were differentially expressed during drought treatment. Co-expression network analysis identified a potential drought regulatory network between cytochrome P450 genes (Unigene4122_c1_g1) and a core regulatory transcription factor Unigene9098_c3_g1 (PsNAC1) with highly significant expression differences. We validated PsNAC1 overexpression in Arabidopsis and demonstrated enhanced drought resistance. CONCLUSIONS: These findings provide insight into the molecular basis of drought resistance in P. sylvestris var. mongolica and lay the foundation for further exploration of its regulatory network.

[Analysis and Evaluation of Heavy Metal Pollution in Farmland Soil in China：A Meta-analysis].

In this study, a Meta-analysis was used to investigate the pollution status of eight farmland soil heavy metal elements (As, Cd, Cr, Cu, Hg, Ni, Pb, and Zn) in China. Meanwhile, their spatiotemporal changes and differences between different types of cultivated land were explored. The research data were chosen from 449 relevant literature data collected by CNKI and Web of Science from 2005 to 2021, and the Meta-analysis used a weighted method based on "sampling numbers", "study area", and "standard deviation". The results showed that the national average values of the eight heavy metal elements in Chinese farmland soil were ω(As)11.00 mg·kg-1, ω(Cd)0.350 2 mg·kg-1, ω(Cr)62.91 mg·kg-1, ω(Cu)28.87 mg·kg-1, ω(Hg)0.135 1 mg·kg-1, ω(Ni)28.91 mg·kg-1, ω(Pb)34.67 mg·kg-1,and ω(Zn)90.24 mg·kg-1. Compared with their background values, all elements except As accumulated to some extent, and Cd and Hg accumulated the most, exceeding their background values by 177.9% and 340.3%, respectively. The research results indicated that Cd and Hg were the main pollution elements in farmland soil in China, and their accumulation was mainly influenced by human activities. In terms of their temporal and spatial changes, the Yunnan-Guizhou Plateau and the eastern coast were the most concentrated areas of pollution cases, and the pollution center shifted from the middle reaches of the Yangtze River to the southwest over time. The accumulation of heavy metals in farmland soil was affected by crop planting types, and the accumulation of heavy metals in vegetable and paddy soil was significantly greater than that in other cultivated land types.

Temporal dynamics of genetic architecture governing leaf development in Populus.

Leaf development is a multifaceted and dynamic process orchestrated by a myriad of genes to shape the proper size and morphology. The dynamic genetic network underlying leaf development remains largely unknown. Utilizing a synergistic genetic approach encompassing dynamic genome-wide association study (GWAS), time-ordered gene co-expression network (TO-GCN) analyses and gene manipulation, we explored the temporal genetic architecture and regulatory network governing leaf development in Populus. We identified 42 time-specific and 18 consecutive genes that displayed different patterns of expression at various time points. We then constructed eight TO-GCNs that covered the cell proliferation, transition, and cell expansion stages of leaf development. Integrating GWAS and TO-GCN, we postulated the functions of 27 causative genes for GWAS and identified PtoGRF9 as a key player in leaf development. Genetic manipulation via overexpression and suppression of PtoGRF9 revealed its primary influence on leaf development by modulating cell proliferation. Furthermore, we elucidated that PtoGRF9 governs leaf development by activating PtoHB21 during the cell proliferation stage and attenuating PtoLD during the transition stage. Our study provides insights into the dynamic genetic underpinnings of leaf development and understanding the regulatory mechanism of PtoGRF9 in this dynamic process.

Identification of High Tolerance to Jujube Witches' Broom in Indian Jujube (Ziziphus mauritiana Lam.) and Mining Differentially Expressed Genes Related to the Tolerance through Transcriptome Analysis.

The jujube witches' broom (JWB) disease is a severe threat to jujube trees, with only a few cultivars being genuinely tolerant or resistant to phytoplasma. The defense mechanism of jujube trees against phytoplasma is still unclear. In this study, we aimed to investigate the tolerance mechanism of Indian jujube 'Cuimi' to JWB and identify the key genes that contribute to JWB high tolerance. Based on the symptoms and phytoplasma concentrations after infection, we confirmed the high tolerance of 'Cuimi' to JWB. Comparative transcriptome analysis was subsequently performed between 'Cuimi' and 'Huping', a susceptible cultivar of Chinese jujube. Unique gene ontology (GO) terms were identified in 'Cuimi', such as protein ubiquitination, cell wall biogenesis, cell surface receptor signaling pathway, oxylipin biosynthetic process, and transcription factor activity. These terms may relate to the normal development and growth of 'Cuimi' under phytoplasma infection. We identified 194 differential expressed genes related to JWB high tolerance, involved in various processes, such as reactive oxygen species (ROS), Ca2+ sensors, protein kinases, transcription factors (TFs), lignin, and hormones. Calmodulin-like (CML) genes were significantly down-regulated in infected 'Cuimi'. We speculated that the CML gene may act as a negative regulatory factor related to JWB high tolerance. Additionally, the cinnamoyl-CoA reductase-like SNL6 gene was significantly up-regulated in infected 'Cuimi', which may cause lignin deposition, limit the growth of phytoplasma, and mediate immune response of 'Cuimi' to phytoplasma. Overall, this study provides insights into the contribution of key genes to the high tolerance of JWB in Indian jujube 'Cuimi'.

The Key Metabolic Network and Genes Regulating the Fresh Fruit Texture of Jujube (Ziziphus jujuba Mill.) Revealed via Metabolomic and Transcriptomic Analysis.

The texture of fresh jujube fruit is related to its popularity and commercial value. The metabolic networks and essential genes that regulate the texture of jujube (Ziziphus jujuba) fruit are still unknown. In this study, two jujube cultivars with significantly different textures were selected by a texture analyzer. The four developmental stages of the exocarp and mesocarp of jujube fruit were studied separately using metabolomic and transcriptomic analyses. Differentially accumulated metabolites were enriched in several critical pathways related to cell wall substance synthesis and metabolism. Transcriptome analysis confirmed this by finding enriched differential expression genes in these pathways. Combined analysis showed that 'Galactose metabolism' was the most overlapping pathway in two omics. Genes such as ß-Gal, MYB and DOF may affect fruit texture by regulating cell wall substances. Overall, this study provides an essential reference for the establishment of texture-related metabolic and gene networks of jujube fruit.

HPLC-MS/MS-based and transcriptome analysis reveal the effects of ABA and MeJA on jujube (Ziziphus jujuba Mill.) cracking.

Fruit cracking is a physiological disease that occurs during the development of jujube, abscisic acid (ABA) and jasmonic acid (JA) mainly regulate the cell wall metabolic pathway and induce fruit cracking. Here, we used high-performance liquid chromatography-tandem mass spectrometry (HPLC-MS/MS) to detect phytohormone-related metabolites at different developmental stages in cracking-susceptible (CS-15) and cracking-resistant (CR-04) individuals of full-sibling hybrid offspring. The fruit of 'Pingshunbenzao' jujube was treated with ABA and MeJA at the white-ripening stage, and the 48-h fruit cracking index was significantly increased compared to that of CK (water). Furthermore, RNA-seq of semi-red stage fruits identified several differentially expressed genes, related to the cell wall, such as SBT1.7 (Contig21.0.484), EXPA (Contig12.0.7) and QRT3 (newGene_1935), and transcription factors (TFs). These results reveal the relationship between the levels of different hormones and fruit cracking, identify genes associated with fruit cracking, and provide new insights to solve the problem of fruit cracking through hormonal regulation.

Genetic Architecture of Heterophylly: Single and Multi-Leaf Genome-Wide Association Mapping in Populus euphratica.

Heterophylly is an adaptive strategy used by some plants in response to environmental changes. Due to the lack of representative plants with typical heteromorphic leaves, little is known about the genetic architecture of heterophylly in plants and the genes underlying its control. Here, we investigated the genetic characteristics underlying changes in leaf shape based on the model species, Populus euphratica, which exhibits typical heterophylly. A set of 401,571 single-nucleotide polymorphisms (SNPs) derived from whole-genome sequencing of 860 genotypes were associated with nine leaf traits, which were related to descriptive and shape data using single- and multi-leaf genome-wide association studies (GWAS). Multi-leaf GWAS allows for a more comprehensive understanding of the genetic architecture of heterophylly by considering multiple leaves simultaneously. The single-leaf GWAS detected 140 significant SNPs, whereas the multi-leaf GWAS detected 200 SNP-trait associations. Markers were found across 19 chromosomes, and 21 unique genes were implicated in traits and serve as potential targets for selection. Our results provide novel insights into the genomic architecture of heterophylly, and provide candidate genes for breeding or engineering P. euphratica. Our observations also improve understanding of the intrinsic mechanisms of plant growth, evolution, and adaptation in response to climate change.

Comparative Transcriptomic Analyses of Different Jujube Cultivars Reveal the Co-Regulation of Multiple Pathways during Fruit Cracking.

Fruit cracking is a common physiological disorder in many fruit species. Jujube (Ziziphus jujuba Mill.) is an economically valuable fruit in which fruit cracking seriously affects fruit yield and quality and causes significant economic losses. To elucidate cracking-related molecular mechanisms, the cracking-susceptible cultivars 'Cuizaohong' and 'Jinsixiaozao' and the cracking-resistant cultivar 'Muzao' were selected, and comparative transcriptome analyses of cracking and non-cracking 'Cuizaohong' (CC and NC), cracking and non-cracking 'Jinsixiaozao' (CJ and NJ), and non-cracking 'Muzao' (NM) were conducted. A total of 131 differentially expressed genes (DEGs) were common to the CC vs. NC and CJ vs. NJ comparisons. To avoid passive processes after fruit cracking, we also mainly focused on the 225 gradually downregulated DEGs in the CJ, NJ, and NM samples. The functional annotation of the candidate DEGs revealed that 61 genes related to calcium, the cell wall, the cuticle structure, hormone metabolism, starch/sucrose metabolism, transcription factors, and water transport were highly expressed in cracking fruits. We propose that expression-level changes in these genes might increase the turgor pressure and weaken mechanical properties, ultimately leading to jujube fruit cracking. These results may serve as a rich genetic resource for future investigations on fruit cracking mechanisms in jujube and in other fruit species.

The Chinese pine genome and methylome unveil key features of conifer evolution.

Conifers dominate the world's forest ecosystems and are the most widely planted tree species. Their giant and complex genomes present great challenges for assembling a complete reference genome for evolutionary and genomic studies. We present a 25.4-Gb chromosome-level assembly of Chinese pine (Pinus tabuliformis) and revealed that its genome size is mostly attributable to huge intergenic regions and long introns with high transposable element (TE) content. Large genes with long introns exhibited higher expressions levels. Despite a lack of recent whole-genome duplication, 91.2% of genes were duplicated through dispersed duplication, and expanded gene families are mainly related to stress responses, which may underpin conifers' adaptation, particularly in cold and/or arid conditions. The reproductive regulation network is distinct compared with angiosperms. Slow removal of TEs with high-level methylation may have contributed to genomic expansion. This study provides insights into conifer evolution and resources for advancing research on conifer adaptation and development.

Modeling genome-wide by environment interactions through omnigenic interactome networks.

How genes interact with the environment to shape phenotypic variation and evolution is a fundamental question intriguing to biologists from various fields. Existing linear models built on single genes are inadequate to reveal the complexity of genotype-environment (G-E) interactions. Here, we develop a conceptual model for mechanistically dissecting G-E interplay by integrating previously disconnected theories and methods. Under this integration, evolutionary game theory, developmental modularity theory, and a variable selection method allow us to reconstruct environment-induced, maximally informative, sparse, and casual multilayer genetic networks. We design and conduct two mapping experiments by using a desert-adapted tree species to validate the biological application of the model proposed. The model identifies previously uncharacterized molecular mechanisms that mediate trees' response to saline stress. Our model provides a tool to comprehend the genetic architecture of trait variation and evolution and trace the information flow of each gene toward phenotypes within omnigenic networks.

Comparative transcriptome profiling reveals cold stress responsiveness in two contrasting Chinese jujube cultivars.

BACKGROUND: Low temperature is a major factor influencing the growth and development of Chinese jujube (Ziziphus jujuba Mill.) in cold winter and spring. Little is known about the molecular mechanisms enabling jujube to cope with different freezing stress conditions. To elucidate the freezing-related molecular mechanism, we conducted comparative transcriptome analysis between 'Dongzao' (low freezing tolerance cultivar) and 'Jinsixiaozao' (high freezing tolerance cultivar) using RNA-Seq. RESULTS: More than 20,000 genes were detected at chilling (4 °C) and freezing (- 10 °C, - 20 °C, - 30 °C and - 40 °C) stress between the two cultivars. The numbers of differentially expressed genes (DEGs) between the two cultivars were 1831, 2030, 1993, 1845 and 2137 under the five treatments. Functional enrichment analysis suggested that the metabolic pathway, response to stimulus and catalytic activity were significantly enriched under stronger freezing stress. Among the DEGs, nine participated in the Ca2+ signal pathway, thirty-two were identified to participate in sucrose metabolism, and others were identified to participate in the regulation of ROS, plant hormones and antifreeze proteins. In addition, important transcription factors (WRKY, AP2/ERF, NAC and bZIP) participating in freezing stress were activated under different degrees of freezing stress. CONCLUSIONS: Our research first provides a more comprehensive understanding of DEGs involved in freezing stress at the transcriptome level in two Z. jujuba cultivars with different freezing tolerances. These results may help to elucidate the molecular mechanism of freezing tolerance in jujube and also provides new insights and candidate genes for genetically enhancing freezing stress tolerance.

Transcriptome profiling of PeCRY1 transgenic Populus tomentosa.

Cryptochromes, a class of blue light photoreceptors, play vital roles in regulating growth and development in higher plants. Despite their control over various important traits, there have been few studies focusing on cryptochromes in forest trees to date. In this study, the Euphrates poplar (Populus euphratica) gene PeCRY1 (cryptochrome 1 of Populus euphratica) was isolated and heterologously expressed in Populus tomentosa. Three biological replicates of each of the PeCRY1 transgenic P. tomentosa (CRY1) and wild-type (WT) plants were processed for transcriptome profiling. We found 34792 commonly expressed transcripts among the 93868 detected unigenes. Using R package DESeq, we identified 357 differentially expressed genes (DEGs), including 132 upregulated and 225 downregulated genes. Gene ontology (GO) enrichment and KEGG pathway enrichment were used to better understand the functions of detected DEGs. Biosynthetic processes, such as starch and sucrose metabolism, which are closely related to growth and development, were highly enriched. Organic cyclic compound biosynthesis was downregulated, whereas carbohydrate metabolism was upregulated. Through KEGG pathway enrichment, we observed that the pentose phosphate pathway, photosynthesis, and circadian rhythm were significantly enriched. Another method of expression analysis based on quantitative reverse transcription polymerase chain reaction (qRT-PCR) validated our RNA sequencing (RNA-seq) results.

Mapping morphological shape as a high-dimensional functional curve.

Detecting how genes regulate biological shape has become a multidisciplinary research interest because of its wide application in many disciplines. Despite its fundamental importance, the challenges of accurately extracting information from an image, statistically modeling the high-dimensional shape and meticulously locating shape quantitative trait loci (QTL) affect the progress of this research. In this article, we propose a novel integrated framework that incorporates shape analysis, statistical curve modeling and genetic mapping to detect significant QTLs regulating variation of biological shape traits. After quantifying morphological shape via a radius centroid contour approach, each shape, as a phenotype, was characterized as a high-dimensional curve, varying as angle θ runs clockwise with the first point starting from angle zero. We then modeled the dynamic trajectories of three mean curves and variation patterns as functions of θ. Our framework led to the detection of a few significant QTLs regulating the variation of leaf shape collected from a natural population of poplar, Populus szechuanica var tibetica. This population, distributed at altitudes 2000-4500 m above sea level, is an evolutionarily important plant species. This is the first work in the quantitative genetic shape mapping area that emphasizes a sense of 'function' instead of decomposing the shape into a few discrete principal components, as the majority of shape studies do.

The genetic architecture of shoot-root covariation during seedling emergence of a desert tree, Populus euphratica.

The coordination of shoots and roots is critical for plants to adapt to changing environments by fine-tuning energy production in leaves and the availability of water and nutrients from roots. To understand the genetic architecture of how these two organs covary during developmental ontogeny, we conducted a mapping experiment using Euphrates poplar (Populus euphratica), a so-called hero tree able to grow in the desert. We geminated intraspecific F1 seeds of Euphrates Poplar individually in a tube to obtain a total of 370 seedlings, whose shoot and taproot lengths were measured repeatedly during the early stage of growth. By fitting a growth equation, we estimated asymptotic growth, relative growth rate, the timing of inflection point and duration of linear growth for both shoot and taproot growth. Treating these heterochronic parameters as phenotypes, a univariate mapping model detected 19 heterochronic quantitative trait loci (hQTLs), of which 15 mediate the forms of shoot growth and four mediate taproot growth. A bivariate mapping model identified 11 pleiotropic hQTLs that determine the covariation of shoot and taproot growth. Most QTLs detected reside within the region of candidate genes with various functions, thus confirming their roles in the biochemical processes underlying plant growth.

A QTL model to map the common genetic basis for correlative phenotypic plasticity.

As an important mechanism for adaptation to heterogeneous environment, plastic responses of correlated traits to environmental alteration may also be genetically correlated, but less is known about the underlying genetic basis. We describe a statistical model for mapping specific quantitative trait loci (QTLs) that control the interrelationship of phenotypic plasticity between different traits. The model is constructed by a bivariate mixture setting, implemented with the EM algorithm to estimate the genetic effects of QTLs on correlative plastic response. We provide a series of procedure that test (1) how a QTL controls the phenotypic plasticity of a single trait; and (2) how the QTL determines the correlation of environment-induced changes of different traits. The model is readily extended to test how epistatic interactions among QTLs play a part in the correlations of different plastic traits. The model was validated through computer simulation and used to analyse multi-environment data of genetic mapping in winter wheat, showing its utilization in practice.

Allotetraploid and autotetraploid models of linkage analysis.

As a group of important plant species in agriculture and biology, polyploids have been increasingly studied in terms of their genome structure and organization. There are two types of polyploids, allopolyploids and autopolyploids, each resulting from a different genetic origin, which undergo meiotic divisions of a distinct complexity. A set of statistical models has been developed for linkage analysis, respectively for each type, by taking into account their unique meiotic behavior, i.e. preferential pairing for allopolyploids and double reduction for autopolyploids. We synthesized these models and modified them to accommodate the linkage analysis of less informative dominant markers. By reanalysing a published data set of varying ploidy in Arabidopsis, we corrected the estimates of the meiotic recombination frequency aimed to study the significance of polyploidization.

An open-pollinated design for mapping imprinting genes in natural populations.

With the increasing recognition of its role in trait and disease development, it is crucial to account for genetic imprinting to illustrate the genetic architecture of complex traits. Genetic mapping can be innovated to test and estimate effects of genetic imprinting in a segregating population derived from experimental crosses. Here, we describe and assess a design for imprinting detection in natural plant populations. This design is to sample maternal plants at random from a natural population and collect open-pollinated (OP) seeds randomly from each maternal plant and germinate them into seedlings. A two-stage hierarchical platform is constructed to jointly analyze maternal and OP progeny markers. Through tracing the segregation and transmission of alleles from the parental to progeny generation, this platform allows parent-of-origin-dependent gene expression to be discerned, providing an avenue to estimate the effect of imprinting genes on a quantitative trait. The design is derived to estimate imprinting effects expressed at the haplotype level. Its usefulness and utilization were validated through computer simulation. This OP-based design provides a tool to detect the genomic distribution and pattern of imprinting genes as an important component of heritable variation that is neglected in traditional genetic studies of complex traits.

Cloning of the cryptochrome-encoding PeCRY1 gene from Populus euphratica and functional analysis in Arabidopsis.

Cryptochromes are photolyase-like blue/UV-A light receptors that evolved from photolyases. In plants, cryptochromes regulate various aspects of plant growth and development. Despite of their involvement in the control of important plant traits, however, most studies on cryptochromes have focused on lower plants and herbaceous crops, and no data on cryptochrome function are available for forest trees. In this study, we isolated a cryptochrome gene, PeCRY1, from Euphrates poplar (Populus euphratica), and analyzed its structure and function in detail. The deduced PeCRY1 amino acid sequence contained a conserved N-terminal photolyase-homologous region (PHR) domain as well as a C-terminal DQXVP-acidic-STAES (DAS) domain. Secondary and tertiary structure analysis showed that PeCRY1 shares high similarity with AtCRY1 from Arabidopsis thaliana. PeCRY1 expression was upregulated at the mRNA level by light. Using heterologous expression in Arabidopsis, we showed that PeCRY1 overexpression rescued the cry1 mutant phenotype. In addition, PeCRY1 overexpression inhibited hypocotyl elongation, promoted root growth, and enhanced anthocyanin accumulation in wild-type background seedlings grown under blue light. Furthermore, we examined the interaction between PeCRY1 and AtCOP1 using a bimolecular fluorescence complementation (BiFc) assay. Our data provide evidence for the involvement of PeCRY1 in the control of photomorphogenesis in poplar.