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<jats:sec><jats:title>Introduction</jats:title><jats:p>The highly conserved tubby-like proteins (TLPs) play key roles in animal neuronal development and plant growth. The abiotic stress tolerance function of TLPs has been widely explored in plants, however, little is known about comparative studies of TLPs within crops.</jats:p></jats:sec><jats:sec><jats:title>Methods</jats:title><jats:p>Bioinformatic identification, phylogenetic analysis, Cis-element analysis, expression analysis, Cis-element analysis, expression analysis and so on were explored to analysis the TLP gene family of multiple crops.</jats:p></jats:sec><jats:sec><jats:title>Results</jats:title><jats:p>In this study, a comprehensive analysis of <jats:italic>TLP</jats:italic> genes were carried out in seven crops to explore whether similar function of TLPs in rice could be achieved in other crops. We identified 20, 9, 14, 11, 12, 35, 14 and 13 <jats:italic>TLP</jats:italic> genes in <jats:italic>Glycine max</jats:italic>, <jats:italic>Hordeum vulgare</jats:italic>, <jats:italic>Sorghum bicolor</jats:italic>, <jats:italic>Arabidopsis thaliana</jats:italic>, <jats:italic>Oryza sativa Japonica</jats:italic>, <jats:italic>Triticum aestivum</jats:italic>, <jats:italic>Setaria italic</jats:italic> and <jats:italic>Zea mays</jats:italic>, respectively. All of them were divided into two groups and ten orthogroups (Ors) based on amino acids. A majority of <jats:italic>TLP</jats:italic> genes had two domains, tubby-like domain and F-box domain, while members of Or5 only had tubby-like domain. In addition, Or5 had more exons and shorter DNA sequences, showing that characteristics of different Ors reflected the differentiated function and feature of <jats:italic>TLP</jats:italic> genes in evolutionary process, and Or5 was the most different from the other Ors. Besides, we recognized 25 <jats:italic>cis</jats:italic>-elements in the promoter of <jats:italic>TLP</jats:italic> genes and explored multiple new regulation pathway of TLPs including light and hormone response. The bioinformatic and transcriptomic analysis implied the stresses induced expression and possible functional redundancy of <jats:italic>TLP</jats:italic> genes. We detected the expression level of 6 <jats:italic>OsTLP</jats:italic> genes at 1 to 6 days after seed germination in rice, and the most obvious changes in these days were appeared in <jats:italic>OsTLP10</jats:italic> and <jats:italic>OsTLP12.</jats:italic></jats:p></jats:sec><jats:sec><jats:title>Discussion</jats:title><jats:p>Combined yeast two-hybrid system and pull down assay, we suggested that the <jats:italic>TLP</jats:italic> genes of Or1 may have similar function during seed germination in different species. In general, the results of comprehensive analysis of <jats:italic>TLP</jats:italic> gene family in multiple species provide valuable evolutionary and functional information of <jats:italic>TLP</jats:italic> gene family which are useful for further application and study of <jats:italic>TLP</jats:italic> genes.</jats:p></jats:sec>

<jats:p><jats:italic>Pinus massoniana</jats:italic> is a pioneer tree widely planted for afforestation on barren hills in southern China where the total planted area is 8.04 million ha. The invasive pine wood nematode (<jats:italic>Bursaphelenchus xylophilus</jats:italic>) poses a serious threat to the survival of <jats:italic>P. massoniana</jats:italic>. Plant resistance genes encoded by leucine-rich repeat-containing transmembrane-receptor proteins play important roles in plant defense. Leucine-rich repeat receptor-like kinases (LRR-RLKs), the largest subfamily of the RLK protein family, play an important role in sensing stress signals in plants. However, the LRR-RLKs of <jats:italic>P. massoniana</jats:italic> have not been characterized previously, and their role in resistance to <jats:italic>B. xylophilus</jats:italic> is unknown. In this study, 185 members of the LRR-RLK subfamily were identified in <jats:italic>P. massoniana</jats:italic> and were categorized into 14 subgroups. Transcriptomic and quantitative real-time RT-PCR analyses showed that <jats:italic>PmRLKs32</jats:italic> was highly expressed in the stem tissue after inoculation with <jats:italic>B. xylophilus</jats:italic>. The gene exhibited high homology with <jats:italic>AtFLS2</jats:italic> of <jats:italic>Arabidopsis thaliana</jats:italic>. <jats:italic>PmRLKs32</jats:italic> was localized to the plasma membrane and was significantly upregulated in nematode-resistant and nematode-susceptible individuals. The transient expression of <jats:italic>PmRLKs32</jats:italic> resulted in a burst of reactive oxygen species production in <jats:italic>P. massoniana</jats:italic> and <jats:italic>Nicotiana benthamiana</jats:italic> seedlings. These results lay a foundation for further exploration of the regulatory mechanism of LRR-RLKs in response to biotic stress in <jats:italic>P. massoniana</jats:italic>.</jats:p>

<jats:p>The regulation of reactive oxygen species (ROS) levels in plants is ensured by mechanisms preventing their over accumulation, and by diverse antioxidants, including enzymes and nonenzymatic compounds. These are affected by redox conditions, posttranslational modifications, transcriptional and posttranscriptional modifications, Ca<jats:sup>2+</jats:sup>, nitric oxide (NO) and mitogen-activated protein kinase signaling pathways. Recent knowledge about protein-protein interactions (PPIs) of antioxidant enzymes advanced during last decade. The best-known examples are interactions mediated by redox buffering proteins such as thioredoxins and glutaredoxins. This review summarizes interactions of major antioxidant enzymes with regulatory and signaling proteins and their diverse functions. Such interactions are important for stability, degradation and activation of interacting partners. Moreover, PPIs of antioxidant enzymes may connect diverse metabolic processes with ROS scavenging. Proteins like receptor for activated C kinase 1 may ensure coordination of antioxidant enzymes to ensure efficient ROS regulation. Nevertheless, PPIs in antioxidant defense are understudied, and intensive research is required to define their role in complex regulation of ROS scavenging.</jats:p>

<jats:p>Dihydroflavonol Q 4-reductase (DFR), a key enzyme in the flavonoid biosynthetic pathway in plants, significantly influences plant survival. However, the roles of DFR in the regulation of plant development are largely unknown. In the present study, phenotypes of transgenic tobacco plants overexpressing the <jats:italic>Ginkgo biloba DFR</jats:italic> gene, <jats:italic>GbDFR6</jats:italic>, were investigated. Transgenic tobacco seedlings exhibited relatively low fresh weights, long primary roots, decreased lateral root numbers, and impaired root gravitropic responses when compared to wild-type tobacco plants. Adult transgenic tobacco plants exhibited a considerably high percentage of wrinkled leaves when compared to the wild-type tobacco plants. In addition to the auxin-related phenotypic changes, transgenic tobacco plants exhibited delayed flowering phenotypes under short-day conditions. Gene expression analysis revealed that the delayed flowering in transgenic tobacco plants was caused by the low expression levels of <jats:italic>NtFT4</jats:italic>. Finally, variations in anthocyanin and flavonoid contents in transgenic tobacco plants were evaluated. The results revealed that the levels of most anthocyanins identified in transgenic tobacco leaves increased. Specifically, cyanidin-3,5-<jats:italic>O</jats:italic>-diglucoside content increased by 9.8-fold in transgenic tobacco plants when compared to the wild-type tobacco plants. Pelargonidin-3-<jats:italic>O</jats:italic>-(coumaryl)-glucoside was only detected in transgenic tobacco plants. Regarding flavonoid compounds, one flavonoid compound (epicatechin gallate) was upregulated, whereas seven flavonoid compounds (Tamarixetin-3-<jats:italic>O</jats:italic>-rutinoside; Sexangularetin-3-<jats:italic>O</jats:italic>-glucoside-7-<jats:italic>O</jats:italic>-rhamnoside; Kaempferol-3-<jats:italic>O</jats:italic>-neohesperidoside; Engeletin; 2’-Hydoxy,5-methoxyGenistein-<jats:italic>O</jats:italic>-rhamnosyl-glucoside; Diosmetin; Hispidulin) were downregulated in both transgenic tobacco leaves and roots. The results indicate novel and multiple roles of <jats:italic>GbDFR6</jats:italic> in ginkgo and provide a valuable method to produce a late flowering tobacco variety in tobacco industry.</jats:p>

<jats:p>Reproductive growth is a bioenergetic process with high energy consumption. Pollination induces female flower longevity in spinach by accelerating sepal retention and development. Cellular bioenergetics involved in cellular growth is at the foundation of all developmental activities. By contrast, how pollination alter the sepal cells bioenergetics to support energy requirement and anabolic biomass accumulation for development is less well understood. To investigate pollination-induced energy-associated pathway changes in sepal tissues after pollination, we utilized RNA-sequencing to identify transcripts that were differentially expressed between unpollinated (UNP) and pollinated flower sepals at 12, 48, and 96HAP. In total, over 6756 non-redundant DEGs were identified followed by pairwise comparisons (i.e. UNP vs 12HAP, UNP vs 48HAP, and UNP vs 96HAP). KEGG enrichment showed that the central carbon metabolic pathway was significantly activated after pollination and governed by pivotal energy-associated regulation pathways such as glycolysis, the citric acid cycle, oxidative phosphorylation, photosynthesis, and pentose phosphate pathways. Co-expression networks confirmed the synergistically regulation interactions among these pathways. Gene expression changes in these pathways were not observed after fertilization at 12HAP, but started after fertilization at 48HAP, and significant changes in gene expression occurred at 96HAP when there is considerable sepal development. These results were also supported by qPCR validation. Our results suggest that multiple energy-associated pathways may play a pivotal regulatory role in post-pollination sepal longevity for developing the seed coat, and proposed an energy pathway model regulating sepal retention in spinach.</jats:p>

<jats:p>Revealing plants’ tolerance and transport genes to heavy metal stress play an important role in exploring the potential of phytoremediation. Taking the heavy metal lead (Pb) hyperaccumulator plant <jats:italic>Pogonatherum crinitum</jats:italic> (Thunb.) Kunth as the research object, a hydroponic simulation stress experiment was set up to determine the physiological indicators such as antioxidant enzymes and non-enzymatic antioxidants in the roots of <jats:italic>P. crinitum</jats:italic> under different Pb concentrations (0, 300, 500, 1000, 2000 mg·L<jats:sup>-1</jats:sup>). RNA-Seq was performed, the Unigenes obtained by transcriptome sequencing were enriched and annotated by Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) databases, and the differential expression genes (DEGs) of root were screened and verified by quantitative real-time polymerase chain reaction (qRT-PCR). The results are as follows: with the increase of Pb concentration, superoxide dismutase (SOD), catalase (CAT), and ascorbic acid (AsA) content increased. Peroxidase (POD), malondialdehyde (MDA), and ascorbic acid–glutathione (AsA-GSH) cycles showed low promotion with high inhibition. A total of 38.21 Gb of bases were obtained by transcriptome sequencing, and the base quality of each sample reached Q20 and Q30, accounting for 90%, making the sequencing results reliable. Combined with transcriptome sequencing, functional annotation, and qRT-PCR validation results, 17 root Pb-tolerant genes of <jats:italic>P. crinitum</jats:italic> were screened out, which were related to antioxidation, transportation, and transcription functions. Moreover, qRT-PCR verification results under different Pb stress concentrations were consistent with the transcriptome sequencing results and changes in physiological indicators. In brief, the root of <jats:italic>P. crinitum</jats:italic> can adapt to the Pb stress environment by up-regulating the expression of related genes to regulate the physiological characteristics.</jats:p>

<jats:p>Parthenocarpy is an extremely important trait that revolutionized the worldwide cultivation of cucumber under protected conditions. Pusa Parthenocarpic Cucumber-6 (PPC-6) is one of the important commercially cultivated varieties under protected conditions in India. Understanding the genetics of parthenocarpy, molecular mapping and the development of molecular markers closely associated with the trait will facilitate the introgression of parthenocarpic traits into non-conventional germplasm and elite varieties. The F<jats:sub>1</jats:sub>, F<jats:sub>2</jats:sub> and back-crosses progenies with a non-parthenocarpic genotype, Pusa Uday indicated a single incomplete dominant gene controlling parthenocarpy in PPC-6. QTL-seq comprising of the early parthenocarpy and non-parthenocarpic bulks along with the parental lines identified two major genomic regions, one each in chromosome 3 and chromosome 6 spanning over a region of 2.7 Mb and 7.8 Mb, respectively. Conventional mapping using F<jats:sub>2:3</jats:sub> population also identified two QTLs, <jats:italic>Parth6.1</jats:italic> and <jats:italic>Parth6.2</jats:italic> in chromosome 6 which indicated the presence of a major effect QTL in chromosome 6 determining parthenocarpy in PPC-6. The flanking markers, SSR01148 and SSR 01012 for <jats:italic>Parth6.1</jats:italic> locus and SSR10476 and SSR 19174 for <jats:italic>Parth6.2</jats:italic> locus were identified and can be used for introgression of parthenocarpy through the marker-assisted back-crossing programme. Functional annotation of the QTL-region identified two major genes, <jats:italic>Csa_6G396640</jats:italic> and <jats:italic>Csa_6G405890</jats:italic> designated as probable indole-3-pyruvate monooxygenase YUCCA11 and Auxin response factor 16, respectively associated with auxin biosynthesis as potential candidate genes. <jats:italic>Csa_6G396640</jats:italic> showed only one insertion at position 2179 in the non-parthenocarpic parent. In the case of <jats:italic>Csa_6G405890</jats:italic>, more variations were observed between the two parents in the form of SNPs and InDels. The study provides insight about genomic regions, closely associated markers and possible candidate genes associated with parthenocarpy in PPC-6 which will be instrumental for functional genomics study and better understanding of parthenocarpy in cucumber.</jats:p>

<jats:p>Flag leaf size is a crucial trait influencing plant architecture and yield potential in wheat. A recombinant inbred line (RIL) population derived from the cross of W7268 and Chuanyu 12 was employed to identify quantitative trait loci (QTL) controlling flag leaf length (FLL), flag leaf width (FLW), and flag leaf area (FLA) in six environments and the best linear unbiased estimator (BLUE) datasets. Using a 55 K SNP-based genetic map, six major and stable QTL were detected with 6.33–53.12% of explained phenotypic variation. Except for <jats:italic>QFlw.cib-4B.3</jats:italic>, the other five major QTL were co-located within two intervals on chromosomes 2B and 2D, namely <jats:italic>QFll/Fla.cib-2B</jats:italic> and <jats:italic>QFll/Flw/Fla.cib-2D</jats:italic>, respectively. Their interactions and effects on the corresponding traits and yield-related traits were also assessed based on flanking markers. <jats:italic>QFll/Fla.cib-2B</jats:italic> showed pleiotropic effects on spikelet number per spike (SNS). <jats:italic>QFlw.cib-4B.3</jats:italic> and <jats:italic>QFll/Flw/Fla.cib-2D</jats:italic> had effects on grain number per spike (GNS) and thousand-grain weight (TGW). Comparison analysis suggested that <jats:italic>QFll/Fla.cib-2B</jats:italic> was likely a new locus. Two candidate genes, <jats:italic>TraesCS2B03G0222800</jats:italic> and <jats:italic>TraesCS2B03G0230000</jats:italic>, associated with leaf development within the interval of <jats:italic>QFll/Fla.cib-2B</jats:italic> were identified based on expression-pattern analysis, gene annotation, ortholog analysis, and sequence variation. The major QTL and markers reported here provide valuable information for understanding the genetic mechanism underlying flag leaf size as well as breeding utilization in wheat.</jats:p>

<jats:p>Cold-stored Hami melon is susceptible to chilling injury, resulting in quality deterioration and reduced sales. Pre-storage treatment with chitosan reduces fruit softening and chilling injury in melon; however, the underlying mechanism remains unclear. In this study, Gold Queen Hami melons were treated with 1.5% chitosan solution for 10 min before cold storage at 3°C and then the effect of chitosan was examined on fruit firmness, weight loss, chilling injury, soluble solid content (SSC), pectin, and soluble sugar contents of melon fruit. Also, the enzyme activities and gene expressions related to fruit softening and starch and sucrose metabolism were investigated. Chitosan treatment reduced the fruit softening and chilling injury, maintained the high levels of starch and sucrose contents, and regulated the enzyme activities and gene expressions related to starch and sucrose metabolism. Fruit firmness was significantly positively correlated with sucrose and starch contents. Altogether, we uncovered the potential mechanism of chitosan coating mitigating melon softening and chilling injury through the regulation of starch and sucrose metabolism.</jats:p>