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<jats:p>Heterophylly, the existence of different leaf shapes and sizes on the same plant, has been observed in many flowering plant species. Yet, the genetic characteristics and genetic basis of heterophylly in soybean remain unknown. Here, two populations of recombinant inbred lines (RILs) with distinctly different leaf shapes were used to identify loci controlling heterophylly in two environments. The ratio of apical leaf shape (LSUP) to basal leaf shape (LSDOWN) at the reproductive growth stage (RLS) was used as a parameter for classifying heterophylly. A total of eight QTL were detected for RLS between the two populations and four of them were stably identified in both environments. Among them, <jats:italic>qRLS20</jats:italic> had the largest effect in the JS population, with a maximum LOD value of 46.9 explaining up to 47.2% of phenotypic variance. This locus was located in the same genomic region as the basal leaf shape QTL <jats:italic>qLSDOWN</jats:italic>20 on chromosome 20. The locus <jats:italic>qRLS19</jats:italic> had the largest effect in the JJ population, with a maximum LOD value of 15.2 explaining up to 27.0% of phenotypic variance. This locus was located in the same genomic region as the apical leaf shape QTL <jats:italic>qLSUP</jats:italic>19 on chromosome 19. Four candidate genes for heterophylly were identified based on sequence differences among the three parents of the two mapping populations, RT-qPCR analysis, and gene functional annotation analysis. The QTL and candidate genes detected in this study lay a foundation for further understanding the genetic mechanism of heterophylly and are invaluable in marker-assisted breeding.</jats:p>

<jats:p>Sulfur is essential in plants because of its presence in numerous molecules including the two amino acids, cysteine, and methionine. Cysteine serves also for the synthesis of glutathione and provides sulfur to many other molecules including protein cofactors or vitamins. Plants absorb sulfate from their environment and assimilate it <jats:italic>via</jats:italic> a reductive pathway which involves, respectively, a series of transporters and enzymes belonging to multigenic families. A tight control is needed to adjust each enzymatic step to the cellular requirements because the whole pathway consumes energy and produces toxic/reactive compounds, notably sulfite and sulfide. Glutathione is known to regulate the activity of some intermediate enzymes. In particular, it provides electrons to adenosine 5′-phosphosulfate reductases but also regulates the activity of glutamate-cysteine ligase by reducing a regulatory disulfide. Recent proteomic data suggest a more extended post-translational redox control of the sulfate assimilation pathway enzymes and of some associated reactions, including the synthesis of both sulfur-containing amino acids, cysteine and methionine, and of glutathione. We have summarized in this review the known oxidative modifications affecting cysteine residues of the enzymes involved. In particular, a prominent regulatory role of protein persulfidation seems apparent, perhaps because sulfide produced by this pathway may react with oxidized thiol groups. However, the effect of persulfidation has almost not yet been explored.</jats:p>

<jats:p>Haloxylon ammodendron and <jats:italic>Haloxylon persicum</jats:italic> are important drought-tolerant plants in northwest China. The whole-genome sequencing of <jats:italic>H. ammodendron</jats:italic> and <jats:italic>H. persicum</jats:italic> grown in their natural environment is incomplete, and their transcriptional regulatory network in response to drought environment remains unclear. To reveal the transcriptional responses of <jats:italic>H. ammodendron</jats:italic> and <jats:italic>H. persicum</jats:italic> to an arid environment, we performed single-molecule real-time (SMRT) and Illumina RNA sequencing. In total, 20,246,576 and 908,053 subreads and 435,938 and 210,334 circular consensus sequencing (CCS) reads were identified by SMRT sequencing of <jats:italic>H. ammodendron</jats:italic> and <jats:italic>H. persicum</jats:italic>, and 15,238 and 10,135 unigenes, respectively, were successfully obtained. In addition, 9,794 and 7,330 simple sequence repeats (SSRs) and 838 and 71 long non-coding RNAs were identified. In an arid environment, the growth of <jats:italic>H. ammodendron</jats:italic> was restricted; plant height decreased significantly; basal and branch diameters became thinner and hydrogen peroxide (H<jats:sub>2</jats:sub>O<jats:sub>2</jats:sub>) content and peroxidase (POD) activity were increased. Under dry and wet conditions, 11,803 and 15,217 differentially expressed genes (DEGs) were identified in <jats:italic>H. ammodendron</jats:italic> and <jats:italic>H. persicum</jats:italic>, respectively. There were 319 and 415 DEGs in the signal transduction pathways related to drought stress signal perception and transmission, including the Ca<jats:sup>2+</jats:sup> signal pathway, the ABA signal pathway, and the MAPK signal cascade. In addition, 217 transcription factors (TFs) and 398 TFs of <jats:italic>H. ammodendron</jats:italic> and <jats:italic>H. persicum</jats:italic> were differentially expressed, including FAR1, MYB, and AP2/ERF. Bioinformatic analysis showed that under drought stress, the expression patterns of genes related to active oxygen [reactive oxygen species (ROS)] scavenging, functional proteins, lignin biosynthesis, and glucose metabolism pathways were altered. Thisis the first full-length transcriptome report concerning the responses of <jats:italic>H. ammodendron</jats:italic> and <jats:italic>H. persicum</jats:italic> to drought stress. The results provide a foundation for further study of the adaptation to drought stress. The full-length transcriptome can be used in genetic engineering research.</jats:p>

<jats:p>Chloroplasts are the material basis of photosynthesis, and temperature and light severely affect chloroplast development and thus influence photosynthetic efficiency. This study identified a spontaneous virescent leaf mutant, SC311Y, whose cotyledons and true leaves were yellow and gradually turned green. However, temperature and light affected the process of turning green. In addition, this mutant (except at the seedling stage) had ruffled leaves with white stripes, sterile males, and poorly fertile female flowers. Genetic characteristics analysis revealed that the recessive gene controlled the virescent leaf. Two F<jats:sub>2</jats:sub> populations mapped <jats:italic>v-3</jats:italic> to the interval of 33.54–35.66 Mb on chromosome 3. In this interval, BSA-Seq, RNA-Seq, and cDNA sequence analyses revealed only one nonsynonymous mutation in the <jats:italic>Csa3G042730</jats:italic> gene, which encoded the RNA exosome supercomplex subunit resurrection1 (RST1). <jats:italic>Csa3G042730</jats:italic> was predicted to be the candidate gene controlling the virescent leaf, and the candidate gene may regulate chloroplast development by regulating <jats:italic>plastid division2 (PDV2)</jats:italic>. A transcriptome analysis showed that different factors caused the reduced chlorophyll and carotenoid content in the mutants. To our knowledge, this study is the first report of map-based cloning related to virescent leaf, male-sterile, and chloroplast RNA regulation in cucumber. The results could accelerate the study of the RNA exosome supercomplex for the dynamic regulation of chloroplast RNA.</jats:p>

<jats:p>The fermentation of <jats:italic>Qu</jats:italic> (FQ) could efficiently produce enzymatically modified starch at a low cost. However, it is poorly understood that how FQ influences the waxy maize starch (WMS) structure and the digestion behavior. In this study, WMS was fermented by <jats:italic>Qu</jats:italic> at different time and starches were isolated at each time point, and its physico-chemical properties and structural parameters were determined. Results showed that the resistant starch (RS), amylose content (AC), the average particle size [D(4,3)] the ratio of peaks at 1,022/995 cm<jats:sup>–1</jats:sup>, and the onset temperature of gelatinization (T<jats:sub><jats:italic>o</jats:italic></jats:sub>) were increased significantly after 36 h. Conversely, the crystallinity, the values of peak viscosity (PV), breakdown (BD), gelatinization enthalpy (ΔH), and the phase transition temperature range (ΔT) were declined significantly after 36 h. It is noteworthy that smaller starch granules were appeared at 36 h, with wrinkles on the surface, and the particle size distribution was also changed from one sharp peak to bimodal. We suggested that the formation of smaller rearranged starch granules was the main reason for the pronounced increase of RS during the FQ process.</jats:p>

<jats:p>Plants are often adversely affected by abiotic stresses such as drought, low temperature, and salinity during growth, and plant NAC-like transcription factors are involved in regulating growth and developmental processes in response to stresses such as drought and salinity. In this study, to investigate the function of <jats:italic>AfNAC1</jats:italic>, a co-expression network of <jats:italic>AfNAC1</jats:italic> genes was constructed using gene expression data from the Chinese legume deciduous shrub, <jats:italic>Amorpha fruticosa</jats:italic> Linn. A 576 bp NAC transcription factor (<jats:italic>AfNAC1</jats:italic> gene, MN180266) encoding 191 amino acids was isolated from <jats:italic>Amorpha fruticosa</jats:italic> seedlings by RT-PCR. qRT-PCR showed that the <jats:italic>AfNAC1</jats:italic> gene was expressed in the roots, stems, leaves, and flowers of <jats:italic>Amorpha fruticosa.</jats:italic> However, drought stress significantly increased root expression, and the AfNAC1 protein was localized in the nucleus by green fluorescence detection. This study analyzed the drought resistance of overexpressing tobacco in depth. Under natural drought stress, the chlorophyll and antioxidant enzyme activities of overexpressing plants were significantly higher than those of wild-type (WT) plants, but the MDA content was lower than that of WT; after rehydration the Fv/Fm values of <jats:italic>AfNAC1</jats:italic>-overexpressing tobacco recovered faster than those of wild-type tobacco and rapidly reached the control levels; <jats:italic>AfNAC1</jats:italic> may be involved in the regulation of the photosystem and indirectly in the regulation of the plant in response to drought stress.</jats:p>

<jats:p>Rootstocks are commonly utilized owing to their resistance to abiotic and biotic stress in viticulture. This study evaluated the effects of three rootstocks (1103P, SO4, and 5A) on the Cabernet Sauvignon (CS) vine growth, and their berries and wines flavonoids profiles in four consecutive vintages. The results showed that 1103P increased the pruning weight of CS and decreased the anthocyanin concentration in berries and wines, especially in the vintages with more rainy and cloudy days. 5A tended to decrease the pruning weight of CS and increase the anthocyanin concentration in berries and wines. Orthogonal partial least squares discriminant analysis (OPLS-DA) showed that the concentrations of total anthocyanins, F3’H-anthocyanins, malvidin-3-<jats:italic>O</jats:italic>-glucoside (Mv-glu), and malvidin-3-<jats:italic>O</jats:italic>-acetylglucoside (Mv-acglu) were the key substances affected by the rootstocks in CS berries and were significantly decreased by 1103P. Total anthocyanins, pinotins, Mv-glu, epicatechin, and vitisins were the rootstock-sensitive compounds that commonly differed in wines among the three comparison groups in the two vintages. Furthermore, 1103P brought more brightness to the wine and 5A gave the wine more red tones. In conclusion, rootstock 5A was recommended in the rainy and cloudy climate regions with regard to the berry flavonoids accumulation and the wine color.</jats:p>

<jats:p>Roots of higher plants provide the shoot with nutrients and water. In exchange, they receive photosynthates, which serve both as energy source and building blocks for maintenance and growth. While studies in plant bioenergetics used to focus on photosynthesis, several more recent findings also aroused or renewed interest in energy conversion and allocation in roots. Root building costs were identified as a long-undervalued trait, which turned out to be highly relevant for stress tolerance and nutrient use efficiency. Reduced building costs per root length (e.g., by aerenchyma formation or by increasing the cell size) are beneficial for exploring the soil for nutrient-rich patches, especially in low-input agrosystems. Also, an apparent mismatch was frequently found between the root energy budget in the form of the ATP pool on the one side and the apparent costs on the other side, particularly the costs of membrane transport under stress conditions, e.g., the Na<jats:sup>+</jats:sup> detoxification costs resulting from Na<jats:sup>+</jats:sup> sequestration at the plasma membrane. Ion transport across the plasma membrane (and also endomembranes) is coupled to the proton motive force usually believed to be exclusively generated by H<jats:sup>+</jats:sup> ATPases. Recently, an alternative mechanism, the biochemical pH clamp, was identified which relies on H<jats:sup>+</jats:sup> formation and binding in the apoplast and the cytosol, respectively, driven by metabolism (so-called active buffering). On this background, several aspects of root bioenergetics are discussed. These are (1) root respiration in soil, with a critical view on calorimetric vs. gas exchange measurements; (2) processes of energy conversion in mitochondria with a special focus on the role of the alternative oxidases, which allow adjusting carbon flow through metabolic pathways to membrane transport processes; and (3) energy allocation, in particular to transport across the plasma membrane forming the interface to soil solution. A concluding remark is dedicated to modeling root bioenergetics for optimizing further breeding strategies. Apparent “energy spoilers” may bestow the plant with a yet unidentified advantage only unfolding their beneficial effect under certain environmental conditions.</jats:p>

<jats:p>Although grazing is the most common use of grassland, the ecological function of grassland far exceeds its productivity. Therefore, the protection of plant diversity is of the utmost importance and cannot be ignored. Existing research on the effect of grazing on grassland mainly focuses on grazing intensity and the type of livestock, but the consequences of the timing of the grazing on the vegetation community remains unclear. We investigated plant community characteristics of winter pastures in alpine meadow with different grazing termination times (grazing before and during the grassland greenup periods) in Maqu County, eastern QTP. The results showed that vegetation height, coverage, aboveground biomass and Graminoid biomass were lower in grassland when grazing happened during the greenup period compared to grassland where grazing was terminated before the greenup period. However, the total plant species richness and forbs richness were higher in grassland with grazing during the greenup period compared to grassland without grazing during the greenup period. Our structural equation modeling reveals a potential indirect implication for the total plant species richness and forbs richness of winter pastures mainly through a decrease in the vegetation coverage and grass biomass abundance. Our findings imply that grazing during the grassland greenup period may facilitate the maintenance of plant diversity in winter pastures. These findings have important implications for grassland ecosystem functioning and for the conservation of plant diversity.</jats:p>

<jats:p><jats:italic>Mandevilla</jats:italic> (Apocynaceae) is a greatly appreciated genus in the world ornamental market. In this study, we attempted to address the poor genetic knowledge and the huge taxonomic gaps existing in this genus by analyzing a collection of 55 accessions. After cytometrically determining the triploid genome size (1,512.64 Mb) of a reference sample (variety “Mandevilla 2001”), the plastidial genome (cpDNA, 0.18 Mb) and a draft of the nuclear genome (nuDNA, 207 Mb) were assembled. While cpDNA was effective in reconstructing the phylogenesis of the Apocynaceae family based on a DNA superbarcoding approach, the nuDNA assembly length was found to be only 41% of the haploid genome size (506 Mb, predicted based on the K-mer frequency distribution). Its annotation enabled the prediction of 37,811 amino acid sequences, of which 10,562 resulted full length proteins. Among them, we identified nine proteins whose orthologs (in <jats:italic>Catharanthus roseus</jats:italic>) are involved in the biosynthesis of monoterpene indole alkaloids (MIAs), including catharanthine, tabersonine, and vincadifformine. The nuclear genome draft was also useful to develop a highly informative (average polymorphism information content, PIC = 0.62) set of 23 simple sequence repeat (SSR) markers that was validated on the Mandevilla collection. These results were integrated with cytometric measurements, nuclear ITS1 haplotyping and chloroplast DNA barcoding analyses to assess the origin, divergence and relationships existing among the 55 accessions object of the study. As expected, based on the scarce information available in the literature, the scenario was extremely intricate. A reasonable hypothesis is that most of the accessions represent interspecific hybrids sharing the same species as maternal parent (i.e., <jats:italic>Mandevilla sanderi</jats:italic>).</jats:p>