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<jats:p>In a cross between two homozygous <jats:italic>Brassica napus</jats:italic> plants of synthetic and natural origin, we demonstrate that novel structural genome variants from the synthetic parent cause immediate genome diversification among F1 offspring. Long read sequencing in twelve F1 sister plants revealed five large-scale structural rearrangements where both parents carried different homozygous alleles but the heterozygous F1 genomes were not identical heterozygotes as expected. Such spontaneous rearrangements were part of homoeologous exchanges or segmental deletions and were identified in different, individual F1 plants. The variants caused deletions, gene copy-number variations, diverging methylation patterns and other structural changes in large numbers of genes and may have been causal for unexpected phenotypic variation between individual F1 sister plants, for example strong divergence of plant height and leaf area. This example supports the hypothesis that spontaneous <jats:italic>de novo</jats:italic> structural rearrangements after <jats:italic>de novo</jats:italic> polyploidization can rapidly overcome intense allopolyploidization bottlenecks to re-expand crops genetic diversity for ecogeographical expansion and human selection. The findings imply that natural genome restructuring in allopolyploid plants from interspecific hybridization, a common approach in plant breeding, can have a considerably more drastic impact on genetic diversity in agricultural ecosystems than extremely precise, biotechnological genome modifications.</jats:p>

<jats:p>Phosphatidylethanolamine-binding proteins (PEBP) family plays important roles in regulating plant flowering time and morphogenesis. However, geneme-wide identification and functional analysis of <jats:italic>PEBP</jats:italic> genes in the rigorous short-day plant <jats:italic>Perilla frutescens</jats:italic> (<jats:italic>PfPEBP</jats:italic>) have not been studied. In this study, 10 PfPEBP were identified and divided into three subfamilies based on their phylogenetic relationships: FT-like, TFL1-like and MFT-like. Gene structure analysis showed that all <jats:italic>PfPEBP</jats:italic> genes contain 4 exons and 3 introns. Motifs DPDxP and GIHR essential for anion-binding activity are highly conserved in PfPEBP. A large number of light-responsive elements were detected in promoter regions of <jats:italic>PfPEBP</jats:italic>. Gene expression of <jats:italic>PfFT1</jats:italic> exhibited a diurnal rhythm. It was highly expressed in leaves under the short-day photoperiod, but higher in flowers and seeds under the long-day photoperiod. Overexpression of <jats:italic>PfFT1</jats:italic> in <jats:italic>Arabidopsis thaliana</jats:italic> not only promoted early flowering of Col-0 or Ler, but also rescued the late flowering phenotype of <jats:italic>ft-1</jats:italic> mutant. We concluded that <jats:italic>PfFT1</jats:italic> promotes early flowering by regulating the expression of flowering-related genes <jats:italic>AtAP1</jats:italic>, <jats:italic>AtLFY</jats:italic>, <jats:italic>AtFUL</jats:italic> and <jats:italic>AtSOC1</jats:italic>. In conclusion, our results provided valuable information for elucidating the functions of <jats:italic>PfPEBP</jats:italic> in <jats:italic>P</jats:italic>. <jats:italic>frutescens</jats:italic> and shed light on the promoting effect of <jats:italic>PfFT1</jats:italic> on flowering.</jats:p>

<jats:p>In response to abiotic and biotic stress or experimental treatment(s), foliar concentrations of inorganic nutrients and metabolites often change in concert to maintain a homeostatic balance within the cell’s environment thus allowing normal functions to carry on. Therefore, whenever possible, changes in cellular chemistry, metabolism, and gene expressions should be simultaneously evaluated using a common pool of tissue. This will help advance the knowledge needed to fill the gaps in our understanding of how these variables function together to maintain cellular homeostasis. Currently, foliar samples of trees for total inorganic nutrients and metabolic analyses are often collected at different times and are stored and processed in different ways before analyses. The objective of the present study was to evaluate whether a pool of wet (previously frozen) intact tissue that is used for metabolic and molecular work would also be suitable for analyses of foliar total inorganic nutrients. We compared quantities of nutrients extracted from wet-intact, dried-intact, and dried-ground tissues taken from a common pool of previously frozen foliage of black oak (<jats:italic>Quercus velutina</jats:italic> L.), sugar maple (<jats:italic>Acer saccharum</jats:italic> Marshall), red spruce (<jats:italic>Picea rubens</jats:italic> Sarg.), and white pine (<jats:italic>Pinus strobus</jats:italic> L.). With a few exceptions in the case of hardwoods where concentrations of total Ca, Mg, K, and P extracted from wet-intact tissue were significantly higher than dry tissue, data pooled across all collection times suggest that the extracted nutrient concentrations were comparable among the three tissue preparation methods and all for species. Based on the data presented here, it may be concluded that drying and grinding of foliage may not be necessary for nutrient analyses thus making it possible to use the same pool of tissue for total inorganic nutrients and metabolic and/or genomic analyses. To our knowledge, this is the first report on such a comparison.</jats:p>

<jats:p><jats:italic>Luffa</jats:italic> is an important medicinal and edible vegetable crop of Cucurbitaceae. Strong heterosis effects and strikingly complementary characteristics were found between the two domesticated <jats:italic>Luffa</jats:italic> cultivars, <jats:italic>Luffa acutangula</jats:italic> and <jats:italic>Luffa cylindrica</jats:italic>. To explore the genetic basis underlying their important agronomic traits, we constructed the first interspecific high-density genetic linkage map using a BC<jats:sub>1</jats:sub> population of 110 lines derived from a cross between S1174 (<jats:italic>Luffa acutangula</jats:italic>) and P93075 (<jats:italic>Luffa cylindrica</jats:italic>). The map spanned a total of 2246.74 cM with an average distance of 0.48 cM between adjacent markers. Thereafter, a large-scale field-based quantitative trait loci (QTLs) mapping was conducted for 25 important agronomic traits and 40 significant genetic loci distributed across 11 chromosomes were detected. Notably, a vital QTL (<jats:italic>qID2</jats:italic>) located on chromosome 9 with a minimum distance of 23 kb was identified to be responsible for the internode diameter and explained 11% of the phenotypic variation. <jats:italic>Lac09g006860</jats:italic> (<jats:italic>LacCRWN3</jats:italic>), encoding a nuclear lamina protein involved in the control of nuclear morphology, was the only gene harbored in <jats:italic>qID2</jats:italic>. Sequence alignment showed completely different promoter sequences between the two parental alleles of <jats:italic>LacCRWN3</jats:italic> except for some nonsynonymous single nucleotide polymorphisms (SNPs) in exons, and the expression level in thick-stem P93075 was distinctively higher than that in thin-stem S1174. According to the natural variation analysis of a population of 183 inbred lines, two main haplotypes were found for <jats:italic>LacCRWN3</jats:italic>: the P93075-like and S1174-like, with the former haplotype lines exhibiting significantly thicker internode diameters than those of the latter haplotype lines. It showed that <jats:italic>LacCRWN3</jats:italic>, as the only CRWN3 gene in Cucurbitaceae, was the most likely candidate gene regulating the internode diameter of <jats:italic>Luffa</jats:italic>. Our findings will be beneficial for deciphering the molecular mechanism of key phenotypic traits and promoting maker-assisted breeding in <jats:italic>Luffa</jats:italic>.</jats:p>

<jats:p>Waterlogging stress has a negative influence on agricultural production, particularly for rapeseed yield in a rice-rape rotation field. To alleviate the profound impacts of waterlogging stress on rapeseed production, a new fertilization with calcium peroxide (CaO<jats:sub>2</jats:sub>) was proposed. In this field experiment, with the conventional rape (<jats:italic>Brassica napus</jats:italic> L.) variety fengyou958 (FY958) and early maturing rape variety xiangyou420 (XY420) as materials, waterlogging was imposed from the bud to flowering stage, and three supplies of CaO<jats:sub>2</jats:sub> (0, C1 for the 594 kg hm<jats:sup>-2</jats:sup> and C2 for the 864 kg hm<jats:sup>-2</jats:sup>) were added as basal fertilizer. The results showed that CaO<jats:sub>2</jats:sub> significantly reduced the accumulation of fermentation products in roots and alleviated the peroxidation of leaves. The reduced waterlogging stress promoted the root vigor and agronomic characters, such as branches, plant height and stem diameter, accelerated dry matter and nutrients accumulation, and resulting in 22.7% (C1) to 232.8% (C2) higher grain yields in XY420, and 112.4% (C1) to 291.8% (C2) higher grain yields in FY958, respectively. In conclusion, 594 kg hm<jats:sup>-2</jats:sup> to 864 kg hm<jats:sup>-2</jats:sup> CaO<jats:sub>2</jats:sub> application restored the growth of waterlogged rapeseed leaves, and reduced the anaerobic intensity of root, which enhanced the resistance of plants to waterlogging, and improved crop productivity. In a certain range, the higher CaO<jats:sub>2</jats:sub> application, the more the yield. This study provides a valid method to prevent damage from flooding in crop fields.</jats:p>

<jats:p>Advances in deep learning and transfer learning have paved the way for various automation classification tasks in agriculture, including plant diseases, pests, weeds, and plant species detection. However, agriculture automation still faces various challenges, such as the limited size of datasets and the absence of plant-domain-specific pretrained models. Domain specific pretrained models have shown state of art performance in various computer vision tasks including face recognition and medical imaging diagnosis. In this paper, we propose AgriNet dataset, a collection of 160k agricultural images from more than 19 geographical locations, several images captioning devices, and more than 423 classes of plant species and diseases. We also introduce AgriNet models, a set of pretrained models on five ImageNet architectures: VGG16, VGG19, Inception-v3, InceptionResNet-v2, and Xception. AgriNet-VGG19 achieved the highest classification accuracy of 94% and the highest F1-score of 92%. Additionally, all proposed models were found to accurately classify the 423 classes of plant species, diseases, pests, and weeds with a minimum accuracy of 87% for the Inception-v3 model. Finally, experiments to evaluate of superiority of AgriNet models compared to ImageNet models were conducted on two external datasets: pest and plant diseases dataset from Bangladesh and a plant diseases dataset from Kashmir.</jats:p>

<jats:p>Photosynthetic organisms maintain optimum levels of photosynthetic pigments in response to environmental changes to adapt to the conditions. The identification of cyanobacteria strains that alleviate bleaching has revealed genes that regulate levels of phycobilisome, the main light-harvesting complex. In contrast, the mechanisms of pigment degradation in algae remain unclear, as no nonbleaching strains have previously been isolated. To address this issue, this study attempted to isolate nonbleaching strains of the unicellular red alga <jats:italic>Cyanidioschyzon merolae</jats:italic> after exposure to nitrogen (N)-depletion based on autofluorescence information. After four weeks under N-depletion, 13 cells from 500,000 cells with almost identical pre- and post-depletion chlorophyll a (Chl a) and/or phycocyanin autofluorescence intensities were identified. These nonbleaching candidate strains were sorted <jats:italic>via</jats:italic> a cell sorter, isolated on solid medium, and their post-N-depletion Chl a and phycocyanin levels were analyzed. Chl a levels of these nonbleaching candidate strains were lower at 1–4 weeks of N-depletion similar to the control strains, however, their phycocyanin levels were unchanged. Thus, we successfully isolated nonbleaching <jats:italic>C. merolae</jats:italic> strains in which phycocyanin was not degraded under N-depletion, <jats:italic>via</jats:italic> autofluorescence spectroscopy and cell sorting. This versatile method will help to elucidate the mechanisms regulating pigments in microalgae.</jats:p>

<jats:p>Canonical strigolactones (SLs), such as orobanchol, consist of a tricyclic lactone ring (ABC-ring) connected to a methylbutenolide (D-ring). Tomato plants have been reported to produce not only orobanchol but also various canonical SLs related to the orobanchol structure, including orobanchyl acetate, 7-hydroxyorobanchol isomers, 7-oxoorobanchol, and solanacol. In addition to these, structurally unidentified SL-like compounds known as didehydroorobanchol isomers (DDHs), whose molecular mass is 2 Da smaller than that of orobanchol, have been found. Although the SL biosynthetic pathway in tomato is partially characterized, structural elucidation of DDHs is required for a better understanding of the entire biosynthetic pathway. In this study, three novel canonical SLs with the same molecular mass as DDHs were identified in tomato root exudates. The first was 6,7-didehydroorobanchol, while the other two were not in the DDH category. These two SLs were designated phelipanchol and epiphelipanchol because they induced the germination of <jats:italic>Phelipanche ramosa</jats:italic>, a noxious root parasitic weed of tomato. We also proposed a putative biosynthetic pathway incorporating these novel SLs from orobanchol to solanacol.</jats:p>