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<jats:p>HOX32, a member of the HD-ZIP III family, functions in the leaf morphogenesis and plant photosynthesis. However, the regulatory mechanism of HOX32 in maize has not been studied and the regulatory relationship in photosynthesis is unclear. We conducted a comprehensive study, including phylogenetic analysis, expression profiling at both transcriptome and translatome levels, subcellular localization, tsCUT&amp;amp;Tag, co-expression analysis, and association analysis with agronomic traits on HOX32 for the dissection of the functional roles of HOX32. <jats:italic>ZmHOX32</jats:italic> shows conservation in plants. As expected, maize HOX32 protein is specifically expressed in the nucleus. <jats:italic>ZmHOX32</jats:italic> showed constitutively expression at both transcriptome and translatome levels. We uncovered the downstream target genes of ZmHOX32 by tsCUT&amp;amp;Tag and constructed a cascaded regulatory network combining the co-expression networks. Both direct and indirect targets of ZmHOX32 showed significant gene ontology enrichment in terms of photosynthesis in maize. The association study suggested that <jats:italic>ZmHOX32</jats:italic> plays an important role in regulation of plant architecture. Our results illustrate a complex regulatory network of HOX32 involving in photosynthesis and plant architecture, which deepens our understanding of the phenotypic variation in plants.</jats:p>

<jats:sec><jats:title>Background</jats:title><jats:p>Lignin is a key component of the secondary cell wall of plants, providing mechanical support and facilitating water transport as well as having important impact effects in response to a variety of biological and abiotic stresses.</jats:p></jats:sec><jats:sec><jats:title>Results</jats:title><jats:p>In this study, we identified 104 genes from ten enzyme gene families related to lignin biosynthesis in <jats:italic>Musa acuminata</jats:italic> genome and found the number of <jats:italic>MaCOMT</jats:italic> gene family was the largest, while <jats:italic>MaC3H</jats:italic>s had only two members. <jats:italic>MaPAL</jats:italic>s retained the original members, and the number of <jats:italic>Ma4CL</jats:italic>s in lignin biosynthesis was significantly less than that of flavonoids. Segmental duplication existed in most gene families, except for <jats:italic>MaC3H</jats:italic>s, and tandem duplication was the main way to expand the number of <jats:italic>MaCOMT</jats:italic>s. Moreover, the expression profiles of lignin biosynthesis genes during fruit development, postharvest ripening stages and under various abiotic and biological stresses were investigated using available RNA-sequencing data to obtain fruit ripening and stress response candidate genes. Finally, a co-expression network of lignin biosynthesis genes was constructed by weighted gene co-expression network analysis to elucidate the lignin biosynthesis genes that might participate in lignin biosynthesis in banana during development and in response to stresses.</jats:p></jats:sec><jats:sec><jats:title>Conclusion</jats:title><jats:p>This study systematically identified the lignin biosynthesis genes in the <jats:italic>Musa acuminata</jats:italic> genome, providing important candidate genes for further functional analysis. The identification of the major genes involved in lignin biosynthesis in banana provides the basis for the development of strategies to improve new banana varieties tolerant to biological and abiotic stresses with high yield and high quality.</jats:p></jats:sec>

<jats:p>Glyphosate has been widely used to control <jats:italic>Eleusine indica</jats:italic> and other weeds in South China for many years. Among the most troublesome weeds in South China, <jats:italic>E. indica</jats:italic> can remain alive all year round. However, the influence of temperature on glyphosate efficacy on <jats:italic>E. indica</jats:italic>, especially under days with fluctuating temperature, is unknown. This study evaluated the influence of two temperature regimes on glyphosate efficacy on glyphosate-resistant (R) and -susceptible (S) <jats:italic>E. indica</jats:italic> biotypes. Plants of the R and S biotypes were cultivated under two temperature regimes (high: 30°C/20°C day/night; low: 20°C/15°C day/night). Dose-response experiments showed improved efficacy of glyphosate at the low temperature compared with that at the high temperature for both biotypes. Based on the LD<jats:sub>50</jats:sub> values, the R biotype was 8.9 times more resistant to glyphosate than the S biotype at the high temperature; however, the resistance index (R/S) decreased to 3.1 at the low temperature. At 4 days after glyphosate application, shikimic acid accumulation was greater at the low temperature than at the high temperature in plants of both biotypes, and the increase was higher in plants of the R biotype than in the S biotype. At a sublethal glyphosate dose (R: 400 g ai ha<jats:sup>−1</jats:sup>; S: 200 g ai ha<jats:sup>−1</jats:sup>), plants grown at the low temperature showed a strong decrease in leaf chlorophyll content and Fv/Fm value compared with those of plants grown at the high temperature and the untreated control. At 3 days after treatment, glyphosate absorption was similar between biotypes at the high temperature, but absorption decreased to 64.9% and 53.1% at the low temperature for the R and S biotypes, respectively. For both biotypes, glyphosate translocation from the leaf to the remainder of the plant was reduced at the low temperature compared with that at the high temperature. No differences in glyphosate translocation were observed between biotypes within each temperature regime. This is the first report on the effect of temperature on glyphosate efficacy on <jats:italic>E. indica</jats:italic>, and provides important insights for glyphosate application and resistance management.</jats:p>

<jats:sec><jats:title>Introduction</jats:title><jats:p>Genomic selection is becoming a standard technique in plant breeding and is now being introduced into forest tree breeding. Despite promising results to predict the genetic merit of superior material based on their additive breeding values, many studies and operational programs still neglect non-additive effects and their potential for enhancing genetic gains.</jats:p></jats:sec><jats:sec><jats:title>Methods</jats:title><jats:p>Using two large comprehensive datasets totaling 4,066 trees from 146 full-sib families of white spruce (Picea glauca (Moench) Voss), we evaluated the effect of the inclusion of dominance on the precision of genetic parameter estimates and on the accuracy of conventional pedigree-based (ABLUP-AD) and genomic-based (GBLUP-AD) models.</jats:p></jats:sec><jats:sec><jats:title>Results</jats:title><jats:p>While wood quality traits were mostly additively inherited, considerable non-additive effects and lower heritabilities were detected for growth traits. For growth, GBLUP-AD better partitioned the additive and dominance effects into roughly equal variances, while ABLUP-AD strongly overestimated dominance. The predictive abilities of breeding and total genetic value estimates were similar between ABLUP-AD and GBLUP-AD when predicting individuals from the same families as those included in the training dataset. However, GBLUP-AD outperformed ABLUP-AD when predicting for new unphenotyped families that were not represented in the training dataset, with, on average, 22% and 53% higher predictive ability of breeding and genetic values, respectively. Resampling simulations showed that GBLUP-AD required smaller sample sizes than ABLUP-AD to produce precise estimates of genetic variances and accurate predictions of genetic values. Still, regardless of the method used, large training datasets were needed to estimate additive and non-additive genetic variances precisely.</jats:p></jats:sec><jats:sec><jats:title>Discussion</jats:title><jats:p>This study highlights the different quantitative genetic architectures between growth and wood traits. Furthermore, the usefulness of genomic additive-dominance models for predicting new families should allow practicing mating allocation to maximize the total genetic values for the propagation of elite material.</jats:p></jats:sec>

<jats:sec><jats:title>Introduction</jats:title><jats:p><jats:italic>Galeola lindleyana</jats:italic> is a mycoheterotrophic orchid belonging to the tribe Vanilleae within the subfamily Vanilloideae.</jats:p></jats:sec><jats:sec><jats:title>Methods</jats:title><jats:p>In this study, the <jats:italic>G. lindleyana</jats:italic> plastome was assembled and annotated, and compared with other Vanilleae orchids, revealing the evolutionary variations between the photoautotrophic and mycoheterotrophic plastomes.</jats:p></jats:sec><jats:sec><jats:title>Results</jats:title><jats:p>The <jats:italic>G. lindleyana</jats:italic> plastome was found to include 32 protein-coding genes, 16 tRNA genes and four ribosomal RNA genes, including 11 pseudogenes. Almost all of the genes encoding photosynthesis have been lost physically or functionally, with the exception of six genes encoding ATP synthase and <jats:italic>psaJ</jats:italic> in photosystem I. The length of the <jats:italic>G. lindleyana</jats:italic> plastome has decreased to 100,749 bp, while still retaining its typical quadripartite structure. Compared with the photoautotrophic Vanilloideae plastomes, the inverted repeat (IR) regions and the large single copy (LSC) region of the mycoheterotrophic orchid’s plastome have contracted, while the small single copy (SSC) region has expanded significantly. Moreover, the difference in length between the two <jats:italic>ndh</jats:italic>B genes was found to be 682 bp, with one of them spanning the IRb/SSC boundary. The Vanilloideae plastomes were varied in their structural organization, gene arrangement, and gene content. Even the <jats:italic>Cyrtosia septentrionalis</jats:italic> plastome which was found to be closest in length to the <jats:italic>G. lindleyana</jats:italic> plastome, differed in terms of its gene arrangement and gene content. In the LSC region, the <jats:italic>psb</jats:italic>A, <jats:italic>psb</jats:italic>K, <jats:italic>atp</jats:italic>A and <jats:italic>psa</jats:italic>B retained in the <jats:italic>G. lindleyana</jats:italic> plastome were missing in the <jats:italic>C. septentrionalis</jats:italic> plastome, while, the <jats:italic>mat</jats:italic>K, <jats:italic>rps</jats:italic>16, and <jats:italic>atp</jats:italic>F were incomplete in the <jats:italic>C. septentrionalis</jats:italic> plastome, yet still complete in that of the <jats:italic>G. lindleyana</jats:italic>. Lastly, compared with the <jats:italic>G. lindleyana</jats:italic> plastome, a 15 kb region located in the SSC area between <jats:italic>ndh</jats:italic>B<jats:italic>-rrn</jats:italic>16S was found to be inverted in the <jats:italic>C. septentrionalis</jats:italic> plastome. These changes in gene content, gene arrangment and gene structure shed light on the polyphyletic evolution of photoautotrophic orchid plastomes to mycoheterotrophic orchid plastomes.</jats:p></jats:sec><jats:sec><jats:title>Discussion</jats:title><jats:p>Thus, this study’s decoding of the mycoheterotrophic <jats:italic>G. lindleyana</jats:italic> plastome provides valuable resource data for future research and conservation of endangered orchids.</jats:p></jats:sec>

<jats:p>Grain amaranths are made up of three New World species of pseudo-cereals with C<jats:sub>4</jats:sub> photosynthesis from the dicotyledonous family Amaranthaceae and the genus <jats:italic>Amaranthus</jats:italic>. They originate in two ecoregions of the Americas, namely, the inter-Andean valleys of South America and the volcanic axis and lowlands of Mexico and Central America. These correspond to two centers of domestications for Andean and Mesoamerican crops, with one cultivated species found in the first region and two found in the latter region. To date, no core collection has been made for the grain amaranths in the United States Department of Agriculture (USDA) germplasm system. In this study, our objective was to create a core for the 2,899 gene bank accessions with collection site data by town or farm site of which 1,090 have current geo-referencing of latitude and longitude coordinates. We constituted the core with 260 genotypes of <jats:italic>Amaranthus</jats:italic>, which we evaluated with 90 single-nucleotide polymorphism markers. Our goal was to distinguish between Andean and Mesoamerican gene pools of amaranths, including the cultivated species and three possible progenitor or wild relative ancestors along with two more species in an outgroup. Population structure, clustering, and discriminant analysis for principal components showed that Andean species <jats:italic>Amaranthus caudatus</jats:italic> and <jats:italic>Amaranthus quitensis</jats:italic> shared fewer alleles with Mesoamerican species <jats:italic>Amaranthus cruentus</jats:italic> and <jats:italic>Amaranthus hypochondriacus</jats:italic>, compared to each group individually. <jats:italic>Amaranthus hybridus</jats:italic> was a bridge species that shared alleles with both regions. Molecular markers have the advantage over morphological traits at quickly distinguishing the Andean and Mesoamerican cultivars and have the added benefit of being useful for following inter-species crosses and introgression.</jats:p>

<jats:p>The family Aizoaceae includes ~1880 species and is one of the more diverse groups within Caryophyllales, particularly in arid areas in the western part of southern Africa. Most species are dwarf succulent-leaf shrubs. In response to the harsh climatic conditions prevalent where they occur, many representatives have evolved special reproductive adaptations. These include hygrochastic capsules (mostly found in Mesembryanthemoideae and Ruschioideae), burr-like indehiscent and one-seeded, winged diaspores, and fast germination of seeds after rain. We focused on anatomical features, evolutionary trends, and the ecological significance of various morpho-anatomical structures found in the seeds. The seeds of 132 species from 61 genera were studied, and 18 diagnostic characters were discovered. All studied characters were compared with those of other families from core Caryophyllales. The seed notch and embryo shape were added to the list of characteristics distinguishing major clades within the family. In addition, the presence of longitudinal ridges and a keel on the seed are additional characters of Aizooideae and combined Ruschioideae-Apatesieae, respectively. Puzzle-like borders of testa cells are a common trait in Ruschioideae and Mesembryanthemoideae. Most taxa in Aizoaceae have a thin seed coat, which is the ancestral state within the family. This may facilitate fast germination. We observed several shifts to a medium-thick or thick seed coat in members of Ruschioideae and Acrosanthoideae. These inhabit fire-prone environments (in vegetation types known as <jats:italic>fynbos</jats:italic> and <jats:italic>renosterveld</jats:italic>), where the thickened seed coat may protect against damage by fire. Multi-seeded fruits are the ancestral state within Aizoaceae, with several shifts to one-(two-)seeded xerochastic fruits. The latter are dispersed <jats:italic>via</jats:italic> autochory, zoochory, or anemochory. This trait has evolved mainly in less succulent subfamilies Acrosanthoideae, Aizooideae, and Sesuvioideae. In highly succulent subfamilies Ruschioideae and Mesembryanthemoideae, fruits are almost exclusively multi-seeded and hygrochastic with ombrohydrochoric dispersal. A reduction in the number of seeds within a dispersal unit is rare. Within Apatesieae and Ruschieae, there are also a few unusual genera whose fruits fall apart into one- to two-seeded mericarps (that are mainly dispersed by wind).</jats:p>

<jats:p>Global soft fruit supply chains rely on trustworthy descriptions of product quality. However, crucial criteria such as sweetness and firmness cannot be accurately established without destroying the fruit. Since traditional alternatives are subjective assessments by human experts, it is desirable to obtain quality estimations in a consistent and non-destructive manner. The majority of research on fruit quality measurements analyzed fruits in the lab with uniform data collection. However, it is laborious and expensive to scale up to the level of the whole yield. The “harvest-first, analysis-second” method also comes too late to decide to adjust harvesting schedules. In this research, we validated our hypothesis of using in-field data acquirable <jats:italic>via</jats:italic> commodity hardware to obtain acceptable accuracies. The primary instance that the research concerns is the sugariness of strawberries, described by the juice’s total soluble solid (TSS) content (unit: °Brix or Brix). We benchmarked the accuracy of strawberry Brix prediction using convolutional neural networks (CNN), variational autoencoders (VAE), principal component analysis (PCA), kernelized ridge regression (KRR), support vector regression (SVR), and multilayer perceptron (MLP), based on fusions of image data, environmental records, and plant load information, etc. Our results suggest that: (i) models trained by environment and plant load data can perform reliable prediction of aggregated Brix values, with the lowest RMSE at 0.59; (ii) using image data can further supplement the Brix predictions of individual fruits from (i), from 1.27 to as low up to 1.10, but they by themselves are not sufficiently reliable.</jats:p>