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<jats:p><jats:italic>Salix floderusii</jats:italic> is a rare alpine tree species in the <jats:italic>Salix</jats:italic> genus. Unfortunately, no extensive germplasm identification, molecular phylogeny, and chloroplast genomics of this plant have been conducted. We sequenced the chloroplast (cp) genome of <jats:italic>S. floderusii</jats:italic> for the first time using second-generation sequencing technology. The cp genome was 155,540 bp long, including a large single-copy region (LSC, 84,401 bp), a small single-copy region (SSC, 16,221 bp), and inverted repeat regions (IR, 54,918 bp). A total of 131 genes were identified, including 86 protein genes, 37 tRNA genes, and 8 rRNA genes. The <jats:italic>S. floderusii</jats:italic> cp genome contains 1 complement repeat, 24 forward repeats, 17 palindromic repeats, and 7 reverse repeats. Analysis of the IR borders showed that the IRa and IRb regions of <jats:italic>S. floderusii</jats:italic> and <jats:italic>Salix caprea</jats:italic> were shorter than those of <jats:italic>Salix cinerea</jats:italic>, which may affect plastome evolution. Furthermore, four highly variable regions were found, including the <jats:italic>rpl22</jats:italic> coding region, <jats:italic>psbM/trnD-GUC</jats:italic> non-coding region, <jats:italic>petA/psbJ</jats:italic> non-coding region, and <jats:italic>ycf1</jats:italic> coding region. These high variable regions can be used as candidate molecular markers and as a reference for identifying future <jats:italic>Salix</jats:italic> species. In addition, phylogenetic analysis indicated that the cp genome of <jats:italic>S. floderusii</jats:italic> is sister to <jats:italic>Salix cupularis</jats:italic> and belongs to the Subgenus <jats:italic>Vetrix</jats:italic>. Genes (Sf-<jats:italic>trnI</jats:italic>, Sf-<jats:italic>PpsbA</jats:italic>, <jats:italic>aadA</jats:italic>, Sf-<jats:italic>TpsbA</jats:italic>, Sf-<jats:italic>trnA</jats:italic>) obtained via cloning were inserted into the pBluescript II SK (+) to yield the cp expression vectors, which harbored the selectable marker gene <jats:italic>aadA</jats:italic>. The results of a spectinomycin resistance test indicated that the cp expression vector had been successfully constructed. Moreover, the <jats:italic>aadA</jats:italic> gene was efficiently expressed under the regulation of predicted regulatory elements. The present study provides a solid foundation for establishing subsequent <jats:italic>S. floderusii</jats:italic> cp transformation systems and developing strategies for the genetic improvement of <jats:italic>S. floderusii.</jats:italic></jats:p>

<jats:p>Improving water use efficiency (<jats:italic>WUE</jats:italic>) has been proven to be a prosperous way to produce more grain in drought-prone areas. Transpiration efficiency (<jats:italic>TE</jats:italic>) has been proposed as a criterion for screening cultivars with high <jats:italic>WUE</jats:italic>. This study quantifies the relations of TE to relative soil water content (<jats:italic>RSWC</jats:italic>) gradients using pot experiments and evaluates the capability of the relations of <jats:italic>TE</jats:italic>-<jats:italic>RSWC</jats:italic> on assessing the cultivar performance in field yield and <jats:italic>WUE</jats:italic>. Twelve winter wheat cultivars were grown at 6 <jats:italic>RSWC</jats:italic>, 12.1, 24.2, 36.3, 48.4, 60.5, and 72.6% of field capacity (<jats:italic>FC</jats:italic> = 24.8 g/g) for 33 days in tightly sealed pots preventing soil evaporation. The results showed that <jats:italic>TE</jats:italic> decreased power functionally following the increase in <jats:italic>RSWC</jats:italic> for all cultivars. The relationship could be described as <jats:italic>TE</jats:italic> = <jats:italic>TE <jats:sub><jats:italic>FC</jats:italic></jats:sub></jats:italic> × (<jats:italic>RSWC</jats:italic>) <jats:italic><jats:sup>b</jats:sup></jats:italic>, named <jats:italic>TE</jats:italic>–<jats:italic>RSWC</jats:italic> curve. This curve could be divided into an orderly area where the rank of cultivars was stable when <jats:italic>RSWC</jats:italic> ≤ 12.1% or <jats:italic>RSWC</jats:italic> ≥ 72.6% and a disorderly area where the rank was unstable when 12.1% &amp;lt; <jats:italic>RSWC</jats:italic> &amp;lt; 72.6%. To assess the consistency of pot TE to field yield and <jats:italic>WUE</jats:italic>, the same 12 varieties were grown under rainfed and two irrigations (75 mm at the jointing and flowering stages, respectively). <jats:italic>TE <jats:sub><jats:italic>FC</jats:italic></jats:sub></jats:italic> was found to be positively related to field yield and <jats:italic>WUE</jats:italic> independent of irrigation. TE measured near the wilting point was negatively related to field yield and <jats:italic>WUE</jats:italic>. These results indicated that <jats:italic>TE <jats:sub><jats:italic>FC</jats:italic></jats:sub></jats:italic> could be used as a surrogate for screening high-yield and high-<jats:italic>WUE</jats:italic> cultivars. The consistency and inconsistency can be attributed to the orderly area and disorderly area of the <jats:italic>TE</jats:italic>–<jats:italic>RSWC</jats:italic> curves.</jats:p>

<jats:p>The abscisic acid (ABA) signaling pathway is the key defense mechanism against drought stress in plants. In the pathway, signal transduction among four core proteins, pyrabactin resistance (PYR), protein phosphatase 2C (PP2C), sucrose-non-fermenting-1-related protein kinase 2 (SnRK2), and ABRE binding factor (ABF) leads to altered gene expression kinetics that is driven by an ABA-responsive element (ABRE). A most recent and comprehensive study provided data suggesting that ABA alters the expression kinetics in over 6,500 genes through the ABF-ABRE associations in <jats:italic>Arabidopsis</jats:italic>. Of these genes, termed ABA gene regulatory network (GRN), over 50% contain a single ABRE within 4 kb of the gene body, despite previous findings suggesting that a single copy of ABRE is not sufficient to drive the gene expression. To understand the expression system of the ABA GRN by the single ABRE, a dynamic model of the gene expression for the desiccation 29A (<jats:italic>RD29A</jats:italic>) gene was constructed with ordinary differential equations. Parameter values of molecular-molecular interactions and enzymatic reactions in the model were implemented from the data obtained by previously conducted <jats:italic>in vitro</jats:italic> experiments. On the other hand, parameter values of gene expression and translation were determined by comparing the kinetics of gene expression in the model to the expression kinetics of <jats:italic>RD29A</jats:italic> in real plants. The optimized model recapitulated the trend of gene expression kinetics of <jats:italic>RD29A</jats:italic> in ABA dose–response that were previously investigated. Further analysis of the model suggested that a single ABRE controls the time scale and dynamic range of the ABA-dependent gene expression through the PP2C feedback regulation even though an additional <jats:italic>cis</jats:italic>-element is required to drive the expression. The model construed in this study underpins the importance of a single ABRE in the ABA GRN.</jats:p>

<jats:p>Sex determination in dioecious plants has been broadly and progressively studied with the blooming of genome sequencing and editing techniques. This provides us with a great opportunity to explore the evolution and genetic mechanisms underlining the sex-determining system in dioecious plants. In this study, comprehensively reviewing advances in sex-chromosomes, sex-determining genes, and floral MADS-box genes in dioecious plants, we proposed a convergent model that governs plant dioecy across divergent species using a cascade regulation pathway connecting sex-determining genes and MADS-box genes e.g., B-class genes. We believe that this convergent mechanism of sex determination in dioecious plants will shed light on our understanding of gene regulation and evolution of plant dioecy. Perspectives concerning the evolutionary pathway of plant dioecy are also suggested.</jats:p>

<jats:p>Molecular markers are developed to accelerate deployment of genes for desirable traits segregated in a bi-parental population of recombinant inbred lines (RILs) or doubled haplotype (DH) lines for mapping. However, it would be the most effective if such markers for multiple traits could be identified in an F<jats:sub>2</jats:sub> population. In this study, single nucleotide polymorphisms (SNP) chips were used to identify major genes for heading date and awn in an F<jats:sub>2</jats:sub> population without developing RILs or DH lines. The population was generated from a cross between a locally adapted spring wheat cultivar “Ningmaizi119” and a winter wheat cultivar “Tabasco” with a diverse genetic background. It was found that the dominant <jats:italic>Vrn-D1</jats:italic> allele could make Ningmaizi119 flowered a few months earlier than Tabasco in the greenhouse and without vernalization. The observed effects of the allele were validated in F<jats:sub>3</jats:sub> populations. It was also found that the dominant <jats:italic>Ali-A1</jats:italic> allele for awnless trait in Tabasco or the recessive <jats:italic>ali-A1</jats:italic> allele for awn trait in Ningmaizi119 was segregated in the F<jats:sub>2</jats:sub> population. The allelic variation in the <jats:italic>ALI-A1</jats:italic> gene relies not only on the DNA polymorphisms in the promoter but also on gene copy number, with one copy <jats:italic>ali-A1</jats:italic> in Ningmaizi119 but two copies <jats:italic>Ali-A1</jats:italic> in Tabasco based on RT-PCR results. According to wheat genome sequences, cultivar “Mattis” has two copies <jats:italic>Ali-A1</jats:italic> and cultivar “Spelta” has four copies <jats:italic>Ali-A</jats:italic> in a chromosome that was uncharacterized (ChrUN), in addition to one copy on chromosome 5A. This study rapidly characterized the effects of the dominant <jats:italic>Vrn-D1</jats:italic> allele and identified the haplotype of <jats:italic>Ali-A1</jats:italic> in gene copy number in the F<jats:sub>2</jats:sub> segregation population of common wheat will accelerate their deployment in cycling lines in breeding.</jats:p>

<jats:p>Breeders agree that leaf senescence is a favorable process for wheat seed yield improvement due to the remobilization of leaf nutrients. However, several studies have suggested that staying green may be an important strategy for further increasing wheat yields. In this study, we performed a comparative transcriptome analysis between wheat cultivars CN17 and CN19 after heading and also measured photosynthetic parameters, chlorophyll (Chl) contents, and antioxidant enzyme activities at various time points after heading. The physiological and biochemical indexes revealed that CN17 exhibited a functionally stay-green phenotype while CN19 did not. We identified a total of 24,585 and 34,410 differential expression genes between genotypes at two time-points and between time-points in two genotypes, respectively, and we also found that 3 (37.5%) genes for leaf senescence, 46 (100%) for photosynthesis – antenna protein, 33 (70.21%) for Chl metabolism and 34 (68%) for antioxidative enzyme activity were upregulated in CN17 compared with CN19 during leaf senescence, which could be regulated by the differential expression of <jats:italic>SAG39</jats:italic> (senescence-associated gene 39), while 22 (100%) genes for photosynthesis – antenna proteins, 6 (46.15%) for Chl metabolism and 12 (80%) for antioxidative enzyme activity were upregulated in CN17 compared with CN19 before the onset of leaf senescence. Here, we further clarified the expression profiles of genes associated with a functional stay-green phenotype. This information provides new insight into the mechanism underlying delayed leaf senescence and a new strategy for breeders to improve wheat yields.</jats:p>

<jats:p>Nitrogen (N) is an important contributor in regulating plant growth and development as well as secondary metabolites synthesis, so as to promote the formation of tea quality and flavor. Theanine, polyphenols, and caffeine are important secondary metabolites in tea plant. In this study, the responses of <jats:italic>Camellia sinensis</jats:italic> roots to N deprivation and resupply were investigated by metabolome and RNA-seq analysis. N deficiency induced content increase for most amino acids (AAs) and reduction for the remaining AAs, polyphenols, and caffeine. After N recovery, the decreased AAs and polyphenols showed a varying degree of recovery in content, but caffeine did not. Meanwhile, theanine increased in content, but its related synthetic genes were down-regulated, probably due to coordination of the whole N starvation regulatory network. Flavonoids-related pathways were relatively active following N stress according to KEGG enrichment analysis. Gene co-expression analysis revealed <jats:italic>TCS2</jats:italic>, <jats:italic>AMT1;1</jats:italic>, <jats:italic>TAT2</jats:italic>, <jats:italic>TS</jats:italic>, and <jats:italic>GOGAT</jats:italic> as key genes, and TFs like MYB, bHLH, and NAC were also actively involved in N stress responses in <jats:italic>C. sinensis</jats:italic> roots. These findings facilitate the understanding of the molecular mechanism of N regulation in tea roots and provide genetic reference for improving N use efficiency in tea plant.</jats:p>

<jats:p>Grapevine is regarded as a highly profitable culture, being well spread worldwide and mostly directed to the wine-producing industry. Practices to maintain the vineyard in healthy conditions are tenuous and are exacerbated due to abiotic and biotic stresses, where fungal grapevine trunk diseases (GTDs) play a major role. The abolishment of chemical treatments and the intensification of several management practices led to an uprise in GTD outbreaks. Symptomatology of GTDs is very similar among diseases, leading to underdevelopment of the vines and death in extreme scenarios. Disease progression is widely affected by biotic and abiotic factors, and the prevalence of the pathogens varies with country and region. In this review, the state-of-the-art regarding identification and detection of GTDs is vastly analyzed. Methods and protocols used for the identification of GTDs, which are currently rather limited, are highlighted. The main conclusion is the utter need for the development of new technologies to easily and precisely detect the presence of the pathogens related to GTDs, allowing to readily take phytosanitary measures and/or proceed to plant removal in order to establish better vineyard management practices. Moreover, new practices and methods of detection, identification, and quantification of infectious material would allow imposing greater control on nurseries and plant exportation, limiting the movement of infected vines and thus avoiding the propagation of fungal inoculum throughout wine regions.</jats:p>

<jats:p>Precise and site-specific nitrogen (N) fertilizer management of vegetables is essential to improve the N use efficiency considering temporal and spatial fertility variations among fields, while the current N fertilizer recommendation methods are proved to be time- and labor-consuming. To establish a site-specific N topdressing algorithm for bok choy (<jats:italic>Brassica rapa subsp. chinensis</jats:italic>), using a hand-held GreenSeeker canopy sensor, we conducted field experiments in the years 2014, 2017, and 2020. Two planting densities, viz, high (123,000 plants ha<jats:sup>–1</jats:sup>) in Year I and low (57,000 plants ha<jats:sup>–1</jats:sup>) in Year II, whereas, combined densities in Year III were used to evaluate the effect of five N application rates (0, 45, 109, 157, and 205 kg N ha<jats:sup>–1</jats:sup>). A robust relationship was observed between the sensor-based normalized difference vegetation index (NDVI), the ratio vegetation index (RVI), and the yield potential without topdressing (YP<jats:sub>0</jats:sub>) at the rosette stage, and 81–84% of the variability at high density and 76–79% of that at low density could be explained. By combining the densities and years, the <jats:italic>R</jats:italic><jats:sup>2</jats:sup> value increased to 0.90. Additionally, the rosette stage was identified as the earliest stage for reliably predicting the response index at harvest (RI<jats:sub>Harvest</jats:sub>), based on the response index derived from NDVI (RI<jats:sub>NDVI</jats:sub>) and RVI (RI<jats:sub>RVI</jats:sub>), with <jats:italic>R</jats:italic><jats:sup>2</jats:sup> values of 0.59–0.67 at high density and 0.53–0.65 at low density. When using the combined results, the RI<jats:sub>RVI</jats:sub> performed 6.12% better than the RI<jats:sub>NDVI</jats:sub>, and 52% of the variability could be explained. This study demonstrates the good potential of establishing a sensor-based N topdressing algorithm for bok choy, which could contribute to the sustainable development of vegetable production.</jats:p>

<jats:p>Fertilizer management is vital for sustainable agriculture under climate change. Reduced basal and increased topdressing fertilizer rate (RBIT) has been reported to improve the yield of in–season rice or wheat. However, the effect of RBIT on rice and wheat yield stability and soil organic carbon (SOC) sequestration potential is unknown, especially when combined with straw incorporation. Here, we report the effect of RBIT with/without straw incorporation on crop yields, yield stability, SOC stock, and SOC fractions in the lower Yangtze River rice–wheat system region over nine years. RBIT with/without straw incorporation significantly increased nine–year average and annual rice yields but not wheat yields. Compared with conventional fertilization (<jats:italic>CF</jats:italic>), RBIT did not significantly affect wheat or rice yield stability, but combined with straw incorporation, it increased the sustainable yield index (SYI) of wheat and rice by 7.6 and 12.8%, respectively. RBIT produced a higher C sequestration rate (0.20 Mg C ha<jats:sup>−1</jats:sup> year<jats:sup>−1</jats:sup>) than <jats:italic>CF</jats:italic> (0.06 Mg ha<jats:sup>−1</jats:sup> year<jats:sup>−1</jats:sup>) in the 0–20 cm layer due to higher root C input and lower C mineralization rate, and RBIT in combination with straw incorporation produced the highest C sequestration rate (0.47 Mg ha<jats:sup>−1</jats:sup> year<jats:sup>−1</jats:sup>). Long–term RBIT had a greater positive effect on silt+clay (0.053 mm)–associated C, microbial biomass C (MBC), dissolved organic C, and hot water organic C in the surface layer (0–10 cm) than in the subsurface layer (10–20 cm). In particular, the increases in SOC pools and mean weight diameter (MWD) of soil aggregates were greater when RBIT was combined with straw incorporation. Correlation analysis indicated that topsoil SOC fractions and MWD were positively correlated with the SYI of wheat and rice. Our findings suggest that the long–term application of RBIT combined with straw incorporation contributed to improving the sustainability of rice production and SOC sequestration in a rice–wheat system.</jats:p>