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Pecans are a globally important tree nut crop. Pecan nuts are rich in fatty acids (FAs), proteins, and flavonoids in addition to thiamine and numerous micronutrients. Although several of these nutriments have been studied in this plant, the comprehensive metabolite variations and molecular mechanisms associated with them have not been fully elucidated. In this study, untargeted metabolomics and transcriptomics were integrated to reveal the metabolite accumulation patterns and their associated molecular mechanisms during pecan kernel development. In total, 4260 (under positive mode) and 2726 (under negative mode) high quality features were retained. Overall, 163 differentially accumulated metabolites were identified. Most components were classified into the categories "organic acids and derivatives" and "lipids and lipid-like molecules." The accumulation patterns of amino acids, FAs, carbohydrates, organic acids, vitamins, flavonoids, and phenylpropanoids alongside embryo development were determined. Furthermore, transcriptomes from four pecan kernel developmental stages were used to assess transcript expression levels. Coexpression analyses were performed between FAs and their related genes. This study provides a comprehensive overview of the metabolic changes and regulations during pecan kernel development. We believe that the identification of nutriment accumulation trends and hub genes associated with the biosynthesis of the components will be valuable for genetically improving this plant.

Flavonoids influence the flavor and nutritional value of pecan nuts. However, limited information is available regarding the molecular mechanisms underlying pecan flavonoid biosynthesis. Here, we used a high (“YLC28”) and a low (“Oconee”) flavonoid content cultivar as the research objects. The changes in flavonoid content and the gene transcription patterns during kernel development were identified. Different accumulation patterns of total flavonoids (TF) and condensed tannins (CT) were observed between the two cultivars. The contents of TF and CT in “YLC28” were 1.76- and 2.67-fold higher levels than that of “Oconee” on 150 days after full bloom of female flowers, respectively. In total, 30 RNA-Seq libraries were constructed and sequenced. The upregulated genes in “YLC28” were highly enriched in flavonoid-related pathways. Thirty-three structural genes were identified, and the expression of two phenylalanine ammonia lyases, one chalcone synthase, one flavonoid 3’,5’-hydroxylase, and one flavonol synthase exhibited high correlation (r ≥ 0.7, p < 0.01) with the condensed tannin content in “YLC28.” A putative MYB transcription factor, CIL1093S0100, might act as a flavonoid biosynthesis repressor during kernel development. Altogether, these results will be useful for uncovering the molecular mechanisms of flavonoid biosynthesis and subsequently accelerating quality pecan breeding.

Pecan is rich in bioactive components such as fatty acids (FAs) and flavonoids and is an important nut type worldwide. Therefore, the molecular mechanisms of phytochemical biosynthesis in pecan are a focus of research. Recently, a draft genome and several transcriptomes have been published. However, the full-length mRNA transcripts remain unclear, and the regulatory mechanisms behind the quality components biosynthesis and accumulation have not been fully investigated. In this study, single-molecule long-read sequencing technology was used to obtain full-length transcripts of pecan kernels. In total, 37,504 isoforms of 16,702 genes were mapped to the reference genome. The numbers of known isoforms, new isoforms, and novel isoforms were 9013 (24.03%), 26,080 (69.54%), and 2411 (6.51%), respectively. Over 80% of the transcripts (30,751, 81.99%) had functional annotations. A total of 15,465 alternative splicing (AS) events and 65,761 alternative polyadenylation events were detected; wherein, the retained intron was the predominant type (5652, 36.55%) of AS. Furthermore, 1894 long noncoding RNAs and 1643 transcription factors were predicted using bioinformatics methods. Finally, the structural genes associated with FA and flavonoid biosynthesis were characterized. A high frequency of AS accuracy (70.31%) was observed in FA synthesis-associated genes. This study provides a full-length transcriptome data set of pecan kernels, which will significantly enhance the understanding of the regulatory basis of phytochemical biosynthesis during pecan kernel maturation.

A comprehensive method for evaluating kernel quality was established by estimating in detail the kernel quality of 27 pecan cultivars introduced into China and by exploring the major trait differences among the different cultivars of pecan. The contents of crude fat, crude protein, soluble sugar, and tannin; the fatty acid composition; the amino acid composition; and the mineral element composition of 27 pecan cultivars were analyzed and tested using the national standards for principal component analysis (PCA), and orthogonal partial least-squares discriminant analysis (OPLS-DA) was used to comprehensively evaluate the 34 characteristic indicators. The fatty acids in the kernel were dominated by unsaturated fats, with oleic acid having the highest content relative to linoleic acid; the amino acid composition was dominated by medicinal amino acids; and potassium, magnesium, and calcium were the predominant mineral elements. Systematic cluster analysis revealed that the 27 pecan cultivars could be classified into three categories (relatively optimal, general, and poorest kernel quality) and 21 indexes, including oleic, linoleic, linolenic, crude fat, soluble sugars, aspartic acid, and threonine, served as indexes of the differences among the 27 tested cultivars. Combined with principal component analysis and stepwise regression analysis, a kernel quality evaluation model was established and verified, and reliable evaluation results were obtained. In addition, Nos. 9, 65, 66, 72, 8, and 21, which had the best quality, were further ranked using the probability ranking method within the third category of optimal quality cultivars. There were obvious differences in kernel characteristics among the different cultivars of pecan. Six cultivars with potential to be developed into excellent cultivars were preliminarily screened out. It was found that the organic combination of cluster analysis, principal component analysis, and orthogonal partial least-squares discriminant analysis can provide a reliable method for the quality evaluation of pecans.

Camellia reticulata is a typical Camellia species used for the production of edible oil in Southwest China. Here we analyzed the fatty acid composition and bio-active compounds including tocopherol, sitosterol and squalene in C. reticulata oil. The oil mainly comprises 72.78–75.52% oleic acid, 11.40–12.58% palmitic acid, 6.91–8.01% linoleic acid, 2.29–2.98% stearic acid, 0.33–0.52% linolenic acid. The average content of α-tocopherol, β-sitosterol and squalene in solvent extracted C. reticulata oils from six sites are 27.19 mg per 100 g, 289.47 mg kg−1 and 138.28 mg kg−1, respectively. We also evaluated the effect of elevation, an important environment factor influencing seed oil content, on fatty acid composition and bio-active compounds of C. reticulata oil. The results indicated that only β-sitosterol content showed significant difference at the different elevations.

Camellia oleifera, C. meiocarpa, C. yuhsienensis, and C. chekiangoleosa originate from China and are important non-timber trees used for the production of edible oil in South China. The oils extracted from these four Camellia species from two locations in Zhejiang Province were analyzed for fatty acid composition and metallic element content. The predominant fatty acids and unsaturated fatty acid content were similar, whereas the fatty acid composition in the crude oil extracts was quite different among the four Camellia species examined. The lowest oleic acid content and the highest palmitic and linoleic acids content were found in the oil extract of C. yuhsienensis. The content of metallic elements in the crude camellia oil extract considerably varied among the four Camellia species, and they were found in the following decreasing order: Al > Mg > Ca > Mn > Fe > Zn > Cu. The content of these metallic elements was higher in the crude oil extracts of C. yuhsienensis and C. meiocarpa than in those of C. oleifera and C. chekiangoleosa. More than 90% of metallic elements were removed by refining after alkalizing, washing, and decolorization steps.

The soils in karst regions, with carbonate rocks as the background material, are characterized by two main factors, drought and high calcium levels. Handeliodendron bodinieri (Levl.) Rehd is an endemic plant species in this area of China. However, few studies have been carried out on the adaptation mechanism of H. bodinieri to drought and high calcium soil. To reveal the physiological responses of H. bodinieri to exogenous calcium under drought stress, 10% PEG-6000 was used to simulate drought stress, and the effects of exogenous calcium at different concentrations on the physiology of H. bodinieri seedlings under drought stress were studied. The results showed that drought stress significantly reduced the relative water content and water potential of H. bodinieri seedlings. Malondialdehyde (MDA) content, O2&minus, and H2O2 production rates significantly increased under drought stress. The addition of exogenous calcium significantly reduced MDA content and O2&minus, and H2O2 production rates. Moreover, peroxidase (POD), superoxide dismutase (SOD), catalase (CAT), ascorbic acid peroxidase (APX) and glutathione peroxidase (GPX) activities increased significantly under drought stress. At the same time, the accumulation of osmotic regulators such as soluble sugar, betaine and free proline also increased significantly. The addition of exogenous calcium further increased the activity of antioxidant enzymes and the accumulation of osmotic regulatory substances. Consequently, the oxidative stress and osmotic stress induced by drought decreased. Finally, exogenous calcium enhanced the photosynthetic rate (Pn), stomatal conductance (Gs) and transpiration rate (Tr) of H. bodinieri under drought stress and significantly improved water use efficiency (WUE). This study confirmed that the application of exogenous calcium can enhance the water condition, photosynthetic capacity, osmotic regulation and antioxidant capacity of H. bodinieri under drought stress. Of the treatments, the 10 mmol&middot, L&minus, 1 CaCl2 treatment is more likely to improve survival of H. bodinieri under drought tolerance. This study provides an important reference for describing the adaptation mechanism and appropriate conservation of H. bodinieri under drought and high calcium conditions.

Intensive forest plantation management practices, such as use of inorganic chemical fertilizer and herbicides improve productivity, however, their environmental impacts on plantation soil microbial communities and its interaction pattern remain unclear. In this study, we investigated associations between management practice intensities (nutrient-herbicide, nutrient-mowing and manure-mowing), environmental factors including plant coverage, pH, exchangeable calcium (Ca2+), aluminium ion (Al3+), total organic carbon (TOC), C to N ratio (C/N) and soil moisture (SM), and microbial community structure in Chinese hickory (Carya cathayenses) plantations cultivated on two soil types (calcareous and yellow soils). Our results demonstrated that long-term management practices with different intensities significantly changed certain soil environmental factors, and revealed a significant impact on both α and β-diversity of soil bacterial and fungal communities. Specifically, significant higher values of plant coverage, pH, Ca2+, TOC, C/N and SM and lower value of Al3+ were observed under manure-mowing management. Calcareous soil showed significantly higher pH, Ca2+ and TN contents and lower AP values than yellow soil across all three operating intensities. The bacterial community structure was different between the calcareous and yellow soil, but there was no difference for the fungi. Edaphic properties such as pH, Ca2+, TOC and TN were shown to play crucial roles in microbial community structuring, while vegetation-associated factors (vegetation coverage and Al3+) were correlated with fungal community structure. The complexity of microbe co-occurrence network decreased as management practice intensified. The keystone taxa including Bradyrhizobium, Reyranella and Phaselicystis in bacterial network and Rhizophydium and Microascales in fungal network were only observed under manure-mowing, with ecological functions mainly involved in organic carbon degradation and nitrogen fixation. Our results provide insight into the interactions between management practice intensities and soil microbial community characteristics and have implications for the optimization of sustainable forestry management practices and maintenance of microbial diversity and network complexity in over-managed forest plantations.

Pecan ( Carya illinoinensis) is an important tree nut throughout the world. The high concentration of flavonoid in its kernels makes it an excellent food with health benefits. However, the molecular basis of flavonoid biosynthesis in pecan remains unclear, which hinders quality breeding in this plant. Therefore, in order to find the crucial genes involved in flavonoid biosynthesis, the changes in flavonoid profiles and the transcriptomes of pecan kernels at four developmental stages (late water, gel, dough, and mature stages) were analyzed. As a result, the highest levels of total phenolic, condensed tannin, and flavan-3-ols were observed at the "late water stage". Catechin was the most abundant flavan-3-ol at different development stages. In total, 64 773 unigenes were obtained, and 46 924 (72.44%) unigenes were annotated. After differentially expressed gene (DEG) analysis, 12 750 unique DEGs were identified. Flavonoid-related DEGs of 36 structural genes and eight MYBs were obtained. The structural gene set contained three PALs, three CHSs, two CHIs, one F3H, two F3'Hs, two F3'5'Hs, one DFR, one ANS, two LARs, and two ANRs. The expression patterns of most of the structural genes were consistent with the changes in flavonoid profiles during kernel development. We believe that this RNA-Seq data set will provide valuable resources for unraveling the molecular mechanism of flavonoid metabolism in pecan and will significantly promote genetic studies and quality breeding in this plant.

To explore the molecular basis of Sb tolerance mechanism in plant, a comparative proteomic analysis of both roots and leaves in Miscanthus sinensis has been conducted in combination with physiological and biochemical analyses. M. sinensis seedlings were exposed to different doses of Sb, and both roots and leaves were collected after 3 days of treatment. Two-dimensional gel electrophoresis (2-DE) and image analyses found that 29 protein spots showed 1.5-fold change in abundance in leaves and 19 spots in roots, of which 31 were identified by MALDI-TOF-MS and MALDI-TOF-TOF-MS. Proteins involved in antioxidant defense and stress response generally increased their expression all over the Sb treatments. In addition, proteins relative to transcription, signal transduction, energy metabolism and cell division and cell structure showed a variable expression pattern over Sb concentrations. Overall these findings provide new insights into the probable survival mechanisms by which M. sinensis could be adapting to Sb phytotoxicity.

Research Highlights: The distribution of simple sequence repeat (SSR) motifs in two draft genomes of pecan was evaluated. Sixty-six SSR loci were validated by PCR amplification in pecan. Twenty-two new development markers can be used for genetic study in genus Carya. Background and Objectives: Pecan has good nutritional and health benefits and is an important crop worldwide. However, the genetic research in this species is insufficient. One of the main reasons for this is the lack of enough accurate, convenient, and economical molecular markers. Among different marker types, SSR loci are enormously useful in genetic studies. However, the number of SSRs in C. illinoinensis (Wangenh.) K. Koch is limited. Materials and Methods: The distribution of SSR motifs in the pecan genome was analyzed. Then, the primers for each SSR were designed. To evaluate their availability, 74 SSR loci were randomly selected and amplified in pecan. Finally, 22 new SSRs and eight former ones were picked to evaluate the genetic diversity in 60 pecan genotypes and to determine their transferability in other Carya species. Results: 145,714 and 143,041 SSR motifs were obtained from two draft genomes of &lsquo, 87MX3-2&rsquo, and &lsquo, Pawnee&rsquo, respectively. In total, 9145 candidate primers were obtained. Sixty-six (89.19%) primers amplified the target products. Among the 30 SSRs, 29 loci showed polymorphism in 60 pecan genotypes. The polymorphic information content (PIC) values ranged from 0.012 to 0.906. In total, 26, 25, and 22 SSRs can be used in C. cathayensis Sarg., C. dabieshanensis W. C. Cheng &amp, R. H. Chang, and C. hunanensis W.C. Liu, respectively. Finally, the dendrogram of all individuals was constructed. The results agree with the geographic origin of the four species and the pedigree relationships between different pecan cultivars. Conclusions: The characterization of SSRs in the pecan genome and the new SSRs will promote the progress of genetic study and breeding in pecan, as well as other species of genus Carya.

The spatial and temporal soil moisture distribution is an important control on surface ecological processes in areas with rock outcrops resulting from karst rocky desertification (KRD). To explore the local effects of bare rocks within different seasons, soil moisture was measured in a KRD region (Fuyuan County, Yunnan Province, southwest China) at different depths and in different directions and distances from rock outcrops in both the dry and the wet seasons. The soil moisture north and east of the rocks was higher compared to the other directions and to the control plot. This effect is attributed to the shading by the rocks. The shading effect is evident in all seasons but more pronounced in the dry season. In the wet season, the directional dependency is restricted to the surface layer and the increase in soil moisture with depth is more pronounced around the rocks than at the control plot. This is attributed to precipitation-induced runoff from the rock outcrops infiltrating into the deeper layers at the rock–soil interface. These findings suggest the redistribution of water in the wet season and the spatial variation of evapotranspiration in the dry season are factors controlling the local soil moisture pattern around the rock outcrops.

Water deficit and high calcium (Ca2+) content and are two typical soil characteristics in the Karst region. However, the problem of whether high Ca2+ in Karst calcareous soil could increase drought tolerance in calcicole plants has not been solved. We investigated the ecophysiological responses of Cyclobalanopsis glauca (Thunb.) Oerst. cuttings to short-term drought stress and Ca2+ application. Drought stress (10% PEG-6000) markedly reduced relative water content (RWC) and water potential (WP), and enhanced the levels of reactive oxygen species (ROS) production (H2O2 and O2&bull, &minus, ) and malondialdehyde (MDA) content in C. glauca leaves. Under drought treatment, exogenous Ca2+ application (20 mM CaCl2) markedly increased the RWC and WP, and reduced the H2O2, O2&bull, and MDA content. Furthermore, water deficit induced a significant increase in the activities of antioxidant enzymes such as peroxidase (POD), superoxide dismutase (SOD), catalase (CAT), ascorbate peroxidase (APX), glutathione reductase (GR), and glutathione peroxidase (GPX), and increased the accumulation of osmoregulation substances. External Ca2+ alleviated drought-induced oxidative stress and osmotic stress with further increased activities of antioxidant enzymes, and enhanced the accumulation of osmoregulation substances. In addition, exogenous Ca2+ treatment alleviated the reduction of the photosynthesis rate (Pn), stomatal conductance (Gs), transpiration rate (Tr), and chlorophyll content (SPAD), and further increased water use efficiency (WUE) under drought stress. This study confirms that exogenouos Ca2+ application induces improvements in the water status, osmotic adjustment, antioxidant defense, and photosynthesis efficiency of C. glauca under drought stress.