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<jats:p>Fagaceae species dominate forests and shrublands throughout the Northern Hemisphere, and have been used as models to investigate the processes and mechanisms of adaptation and speciation. Compared with the well-studied genus <jats:italic>Quercus</jats:italic>, genomic data is limited for the tropical-subtropical genus <jats:italic>Castanopsis</jats:italic>. <jats:italic>Castanopsis hystrix</jats:italic> is an ecologically and economically valuable species with a wide distribution in the evergreen broad-leaved forests of tropical-subtropical Asia. Here, we present a high-quality chromosome-scale reference genome of <jats:italic>C. hystrix</jats:italic>, obtained using a combination of Illumina and PacBio HiFi reads with Hi-C technology. The assembled genome size is 882.6 Mb with a contig N50 of 40.9 Mb and a BUSCO estimate of 99.5%, which are higher than those of recently published Fagaceae species. Genome annotation identified 37,750 protein-coding genes, of which 97.91% were functionally annotated. Repeat sequences constituted 50.95% of the genome and LTRs were the most abundant repetitive elements. Comparative genomic analysis revealed high genome synteny between <jats:italic>C. hystrix</jats:italic> and other Fagaceae species, despite the long divergence time between them. Considerable gene family expansion and contraction were detected in <jats:italic>Castanopsis</jats:italic> species. These expanded genes were involved in multiple important biological processes and molecular functions, which may have contributed to the adaptation of the genus to a tropical-subtropical climate. In summary, the genome assembly of <jats:italic>C. hystrix</jats:italic> provides important genomic resources for Fagaceae genomic research communities, and improves understanding of the adaptation and evolution of forest trees.</jats:p>

<jats:p>Under semiarid and warm climates, field practices for climate change adaptation have to be defined in order to modulate grape composition according to the desired wine styles. Under this context, the present study investigated several viticulture practices in cv. Macabeo for Cava production. The experiment was carried out over 3 years in a commercial vineyard located in the province of Valencia (eastern Spain). The techniques tested were (i) vine shading, (ii) double pruning (bud forcing), and (iii) the combined application of soil organic mulching and shading, all of them tested against a control. Double pruning significantly modified phenology and grape composition, improving the wine alcohol-to-acidity ratio and reducing the pH. Similar results were also achieved by shading. However, the shading strategy did not significantly affect yield, unlike double pruning, which reduced vine yield even in the year following its application. Shading alone or in combination with mulching significantly improved the vine water status, suggesting that these techniques can also be used to alleviate water stress. Particularly, we found that the effect of soil organic mulching and canopy shading on stem water potential was additive. Indeed, all the techniques tested were useful for improving wine composition for cava production, but double pruning is only recommended for premium Cava production.</jats:p>

<jats:p>Genomic selection is expected to improve selection efficiency and genetic gain in breeding programs. The objective of this study was to assess the efficacy of predicting the performance of grain sorghum hybrids using genomic information of parental genotypes. One hundred and two public sorghum inbred parents were genotyped using genotyping-by-sequencing. Ninty-nine of the inbreds were crossed to three tester female parents generating a total of 204 hybrids for evaluation at two environments. The hybrids were sorted in to three sets of 77,59 and 68 and evaluated along with two commercial checks using a randomized complete block design in three replications. The sequence analysis generated 66,265 SNP markers that were used to predict the performance of 204 F1 hybrids resulted from crosses between the parents. Both additive (partial model) and additive and dominance (full model) were constructed and tested using various training population (TP) sizes and cross-validation procedures. Increasing TP size from 41 to 163 increased prediction accuracies for all traits. With the partial model, the five-fold cross validated prediction accuracies ranged from 0.03 for thousand kernel weight (TKW) to 0.58 for grain yield (GY) while it ranged from 0.06 for TKW to 0.67 for GY with the full model. The results suggest that genomic prediction could become an effective tool for predicting the performance of sorghum hybrids based on parental genotypes.</jats:p>

<jats:sec><jats:title>Introduction</jats:title><jats:p><jats:italic>Limonium</jats:italic> (L.) <jats:italic>tetragonum</jats:italic> (Thunb.) A. A. Bullock, a halophyte that grows all over the southwest coast of Korea, is a medicinal plant with various pharmacological effects. The salt defense mechanism stimulates the biosynthesis of various secondary metabolites and improves functional substances. In this study, we investigated the optimal NaCl concentration for the growth and enhancement of secondary metabolites in hydroponically grown <jats:italic>L. tetragonum</jats:italic>.</jats:p></jats:sec><jats:sec><jats:title>Methods</jats:title><jats:p>The seedlings grown for 3 weeks in a hydroponic cultivation system were treated with 0-, 25-, 50-, 75-, and 100-mM NaCl in Hoagland’s nutrient solution for 8 weeks. No significant effect on the growth and chlorophyll fluorescence was observed for the NaCl concentrations below 100-mM.</jats:p></jats:sec><jats:sec><jats:title>Results and discussions</jats:title><jats:p>The increase in the NaCl concentration resulted in the decrease in the water potential of the <jats:italic>L. tetragonum</jats:italic> leaves. The Na<jats:sup>+</jats:sup> content accumulated in the aerial part increased rapidly and the content of K<jats:sup>+</jats:sup>, which acts as an antagonist, decreased with the increase in NaCl concentrations in hydroponics. The total amino acid content of <jats:italic>L. tetragonum</jats:italic> decreased compared to the 0-mM NaCl, and most of the amino acid content decreased as the NaCl concentration increased. In contrast, the content of urea, proline (Pro), β-alanine, ornithine, and arginine was increased with an increase in NaCl concentration. The Pro content at 100-mM NaCl accounted for 60% of the total amino acids and was found to be a major osmoregulator as an important component of the salt defense mechanisms. The top five compounds identified in the <jats:italic>L. tetragonum</jats:italic> were classified as flavonoids while the flavanone compound was detected only in the NaCl treatments. A total of four myricetin glycosides were increased in comparison to the 0-mM NaCl. Among the differentially expressed genes, a significantly large change in Gene ontology was seen in the circadian rhythm. NaCl treatment enhanced the flavonoid-based substances of <jats:italic>L. tetragonum</jats:italic>. The optimum NaCl concentration for the enhancement of secondary metabolites of the <jats:italic>L. tetragonum</jats:italic> in the vertical farm-hydroponic cultivation system was 75-mM NaCl.</jats:p></jats:sec>

<jats:p>Pathogenesis-related class 10 (PR-10) proteins play a role in plant growth and development, but the underlying molecular mechanisms are unclear. Here, we isolated a salt-induced <jats:italic>PR-10</jats:italic> gene from the halophyte <jats:italic>Halostachys caspica</jats:italic> and named it <jats:italic>HcPR10</jats:italic>. <jats:italic>HcPR10</jats:italic> was constitutively expressed during development and HcPR10 localized to the nucleus and cytoplasm. HcPR10-mediated phenotypes including bolting, earlier flowering, increased branch number and siliques per plant are highly correlated with increased cytokinin levels in transgenic Arabidopsis. Meanwhile, increased levels of cytokinin in plants is temporally correlated with HcPR10 expression patterns. Although the expression of cytokinin biosynthesis genes validated was not upregulated, cytokinin-related genes including chloroplast-related genes, cytokinin metabolism and cytokinin responses genes and flowering-related genes were significantly upregulated in the transgenic Arabidopsis compared to the wild type by transcriptome deep sequencing. Analysis of the crystal structure of HcPR10 revealed a <jats:italic>trans</jats:italic>-zeatin riboside (a type of cytokinin) located deep in its cavity, with a conserved conformation and protein–ligand interactions, supporting HcRP10 acts as a cytokinin reservoir. Moreover, HcPR10 in <jats:italic>Halostachys caspica</jats:italic> predominantly accumulated in vascular tissue, the site of long-distance translocation of plant hormones. Collectively, we draw that HcPR10 as a cytokinin reservoir induces cytokinin-related signal transduction in plants, thereby promoting plant growth and development. These findings could provide intriguing insights into the role of HcPR10 proteins in phytohormone regulation in plants and advance our understanding of cytokinin-mediated plant development and could facilitate the breeding of transgenic crops with earlier mature, higher yielding agronomic traits.</jats:p>

<jats:p>Low temperatures (LTs) negatively affect the percentage and rate of cucumber (<jats:italic>Cucumis sativus</jats:italic> L.) seed germination, which has deleterious effects on yield. Here, a genome-wide association study (GWAS) was used to identify the genetic loci underlying low temperature germination (LTG) in 151 cucumber accessions that represented seven diverse ecotypes. Over two years, phenotypic data for LTG i.e., relative germination rate (RGR), relative germination energy (RGE), relative germination index (RGI) and relative radical length (RRL), were collected in two environments, and 17 of the 151 accessions were found to be highly cold tolerant using cluster analysis. A total of 1,522,847 significantly associated single-nucleotide polymorphism (SNP) were identified, and seven loci associated with LTG, on four chromosomes, were detected: <jats:italic>gLTG1.1</jats:italic>, <jats:italic>gLTG1.2</jats:italic>, <jats:italic>gLTG1.3</jats:italic>, <jats:italic>gLTG4.1</jats:italic>, <jats:italic>gLTG5.1</jats:italic>, <jats:italic>gLTG5.2</jats:italic>, and <jats:italic>gLTG6.1</jats:italic> after resequencing of the accessions. Of the seven loci, three, i.e., <jats:italic>gLTG1.2</jats:italic>, <jats:italic>gLTG4.1</jats:italic>, and <jats:italic>gLTG5.2</jats:italic>, showed strong signals that were consistent over two years using the four germination indices, and are thus strong and stable for LTG. Eight candidate genes associated with abiotic stress were identified, and three of them were potentially causal to LTG: <jats:italic>CsaV3_1G044080</jats:italic> (a pentatricopeptide repeat-containing protein) for <jats:italic>gLTG1.2</jats:italic>, <jats:italic>CsaV3_4G013480</jats:italic> (a RING-type E3 ubiquitin transferase) <jats:italic>for gLTG4.1</jats:italic>, and <jats:italic>CsaV3_5G029350</jats:italic> (a serine/threonine-protein kinase) for <jats:italic>gLTG5.2.</jats:italic> The function for <jats:italic>CsPPR</jats:italic> (<jats:italic>CsaV3_1G044080</jats:italic>) in regulating LTG was confirmed, as <jats:italic>Arabidopsis</jats:italic> lines ectopically expressing <jats:italic>CsPPR</jats:italic> showed higher germination and survival rates at 4°C compared to the wild-type, which preliminarily illustrates that <jats:italic>CsPPR</jats:italic> negatively regulates cucumber cold tolerance at the germination stage. This study will provide insights into cucumber LT-tolerance mechanisms and further promote cucumber breeding development.</jats:p>

<jats:p>A cyanobacterium, <jats:italic>Synechocystis</jats:italic> sp. PCC 6803, contains a lipid with triacylglycerol-like TLC mobility but its identity and physiological roles remain unknown. Here, on ESI-positive LC-MS<jats:sup>2</jats:sup> analysis, it is shown that the triacylglycerol-like lipid (lipid X) is related to plastoquinone and can be grouped into two subclasses, X<jats:sub>a</jats:sub> and X<jats:sub>b</jats:sub>, the latter of which is esterified by 16:0 and 18:0. This study further shows that a <jats:italic>Synechocystis</jats:italic> homolog of type-2 diacylglycerol acyltransferase genes, <jats:italic>slr2103</jats:italic>, is essential for lipid X synthesis: lipid X disappears in a <jats:italic>Synechocystis slr2103</jats:italic>-disruptant whereas it appears in an <jats:italic>slr2103</jats:italic>-overexpressing transformant (OE) of <jats:italic>Synechococcus elongatus</jats:italic> PCC 7942 that intrinsically lacks lipid X. The <jats:italic>slr2103</jats:italic> disruption causes <jats:italic>Synechocystis</jats:italic> cells to accumulate plastoquinone-C at an abnormally high level whereas <jats:italic>slr2103</jats:italic> overexpression in <jats:italic>Synechococcus</jats:italic> causes the cells to almost completely lose it. It is thus deduced that <jats:italic>slr2103</jats:italic> encodes a novel acyltransferase that esterifies 16:0 or 18:0 with plastoquinone-C for the synthesis of lipid X<jats:sub>b</jats:sub>. Characterization of the <jats:italic>slr2103</jats:italic>-disruptant in <jats:italic>Synechocystis</jats:italic> shows that <jats:italic>slr2103</jats:italic> contributes to sedimented-cell growth in a static culture, and to bloom-like structure formation and its expansion by promoting cell aggregation and floatation upon imposition of saline stress (0.3-0.6 M NaCl). These observations provide a basis for elucidation of the molecular mechanism of a novel cyanobacterial strategy to acclimatize to saline stress, and one for development of a system of seawater-utilization and economical harvesting of cyanobacterial cells with high-value added compounds, or blooming control of toxic cyanobacteria.</jats:p>

<jats:p>Plant <jats:italic>terpenoid synthase (TPS)</jats:italic> family genes participate in metabolite synthesis, hormones, gossypol, etc. Here, we genome-widely identified <jats:italic>TPS</jats:italic> family genes in 12 land plant species. Four hundred and thirty TPS-related genes were divided into seven subfamilies. The <jats:italic>TPS-c</jats:italic> in Bryophytes was suggested to be the earliest subfamily, followed by the <jats:italic>TPS-e/f</jats:italic> and <jats:italic>TPS-h</jats:italic> presence in ferns. <jats:italic>TPS-a</jats:italic>, the largest number of genes, was derived from monocotyledonous and dicotyledonous plants. Collinearity analysis showed that 38 out of the 76 <jats:italic>TPS</jats:italic> genes in <jats:italic>G. hirsutum</jats:italic> were collinear within <jats:italic>G. arboreum</jats:italic> and <jats:italic>G. raimondii</jats:italic>. Twenty-one <jats:italic>GhTPS-a</jats:italic> genes belong to the cadinene synthase (<jats:italic>GhCDN)</jats:italic> subfamily and were divided into five groups, A, B, C, D, and E. The special <jats:italic>cis</jats:italic>-elements in the promoters of 12 <jats:italic>GhCDN-A</jats:italic> genes suggested that the JA and ethylene signaling pathways may be involved in their expression regulation. When 12 <jats:italic>GhCDN-A</jats:italic> genes were simultaneously silenced through virus-induced gene silencing, the glandular color of <jats:italic>GhCDN-A</jats:italic>-silenced plants was lighter than that of the control, supported by a gossypol content decrease based on HPLC testing, suggesting that <jats:italic>GhCDN-A</jats:italic> subgroup genes participate in gossypol synthesis. According to RNA-seq analysis, gossypol synthesis-related genes and disease-resistant genes in the glandular variety exhibited upregulated expression compared to the glandless variety, whereas hormone signaling-related genes were downregulated. All in all, these results revealed plant <jats:italic>TPS</jats:italic> gene evolution rules and dissected the <jats:italic>TPS</jats:italic> subfamily, <jats:italic>GhCDN-A</jats:italic>, function in gossypol synthesis in cotton.</jats:p>

<jats:p>Gene duplication resulting from whole-genome duplication (WGD), small-scale duplication (SSD), or unequal hybridization plays an important role in the expansion of gene families. Gene family expansion can also mediate species formation and adaptive evolution. Barley (<jats:italic>Hordeum vulgare</jats:italic>) is the world’s fourth largest cereal crop, and it contains valuable genetic resources due to its ability to tolerate various types of environmental stress. In this study, 27,438 orthogroups in the genomes of seven Poaceae were identified, and 214 of them were significantly expanded in barley. The evolutionary rates, gene properties, expression profiles, and nucleotide diversity between expanded and non-expanded genes were compared. Expanded genes evolved more rapidly and experienced lower negative selection. Expanded genes, including their exons and introns, were shorter, they had fewer exons, their GC content was lower, and their first exons were longer compared with non-expanded genes. Codon usage bias was also lower for expanded genes than for non-expanded genes; the expression levels of expanded genes were lower than those of non-expanded genes, and the expression of expanded genes showed higher tissue specificity than that of non-expanded genes. Several stress-response-related genes/gene families were identified, and these genes could be used to breed barley plants with greater resistance to environmental stress. Overall, our analysis revealed evolutionary, structural, and functional differences between expanded and non-expanded genes in barley. Additional studies are needed to clarify the functions of the candidate genes identified in our study and evaluate their utility for breeding barley plants with greater stress resistance.</jats:p>

<jats:p>The contribution of vine cultivation to human welfare as well as the stimulation of basic social and cultural features of civilization has been great. The wide temporal and regional distribution created a wide array of genetic variants that have been used as propagating material to promote cultivation. Information on the origin and relationships among cultivars is of great interest from a phylogenetics and biotechnology perspective. Fingerprinting and exploration of the complicated genetic background of varieties may contribute to future breeding programs. In this review, we present the most frequently used molecular markers, which have been used on <jats:italic>Vitis</jats:italic> germplasm. We discuss the scientific progress that led to the new strategies being implemented utilizing state-of-the-art next generation sequencing technologies. Additionally, we attempted to delimit the discussion on the algorithms used in phylogenetic analyses and differentiation of grape varieties. Lastly, the contribution of epigenetics is highlighted to tackle future roadmaps for breeding and exploitation of <jats:italic>Vitis</jats:italic> germplasm. The latter will remain in the top of the edge for future breeding and cultivation and the molecular tools presented herein, will serve as a reference point in the challenging years to come.</jats:p>