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<jats:p>Yield is the most complex trait to improve crop production, and identifying the genetic determinants for high yield is a major issue in breeding new varieties. In faba bean (<jats:italic>Vicia faba</jats:italic> L.), quantitative trait loci (QTLs) have previously been detected in studies of biparental mapping populations, but the genes controlling the main trait components remain largely unknown. In this study, we investigated for the first time the genetic control of six faba bean yield-related traits: shattering (SH), pods per plant (PP), seeds per pod (SP), seeds per plant (SPL), 100-seed weight (HSW), and plot yield (PY), using a genome-wide association study (GWAS) on a worldwide collection of 352 homozygous faba bean accessions with the aim of identifying markers associated with them. Phenotyping was carried out in field trials at three locations (Spain, United Kingdom, and Serbia) over 2 years. The faba bean panel was genotyped with the Affymetrix faba bean SNP-chip yielding 22,867 SNP markers. The GWAS analysis identified 112 marker–trait associations (MTAs) in 97 candidate genes, distributed over the six faba bean chromosomes. Eight MTAs were detected in at least two environments, and five were associated with multiple traits. The next step will be to validate these candidates in different genetic backgrounds to provide resources for marker-assisted breeding of faba bean yield.</jats:p>

<jats:sec><jats:title>Background</jats:title><jats:p><jats:italic>Thymus mandschuricus</jats:italic> is an aromatic and medicinal plant with notable antibacterial and antioxidant properties. However, traditional breeding methods rely on phenotypic selection due to a lack of molecular resources. A high-quality reference genome is crucial for marker-assisted breeding, genome editing, and molecular genetics.</jats:p></jats:sec><jats:sec><jats:title>Results</jats:title><jats:p>We utilized PacBio and Hi-C technologies to generate a high-quality chromosome-level reference genome for <jats:italic>T. mandschuricus</jats:italic>, with a size of 587.05 Mb and an N50 contig size of 8.41 Mb. The assembled genome contained 29,343 predicted protein-coding genes, and evidence of two distinct whole-genome duplications in <jats:italic>T. mandschuricus</jats:italic> was discovered. Comparative genomic analysis revealed rapid evolution of genes involved in phenylpropanoid biosynthesis and the CYP450 gene family in <jats:italic>T. mandschuricus</jats:italic>. Additionally, we reconstructed the gene families of terpenoid biosynthesis structural genes, such as TPS, BAHD, and CYP, and identified regulatory networks controlling the expression of aroma-synthesis genes by integrating transcriptome data from various organs and developmental stages. We discovered that hormones and transcription factors may collaborate in controlling aroma-synthesis gene expression.</jats:p></jats:sec><jats:sec><jats:title>Conclusion</jats:title><jats:p>This study provides the first high-quality genome sequence and gene annotation for <jats:italic>T. mandschuricus</jats:italic>, an indigenous thyme species unique to China. The genome assembly and the comprehension of the genetic basis of fragrance synthesis acquired from this research could potentially serve as targets for future breeding programs and functional studies.</jats:p></jats:sec>

<jats:p>For the past 300 years, hydrogen sulfide (H<jats:sub>2</jats:sub>S) has been considered a toxic gas. Nowadays, it has been found to be a novel signaling molecule in plants involved in the regulation of cellular metabolism, seed germination, plant growth, development, and response to environmental stresses, including high temperature (HT) and low temperature (LT). As a signaling molecule, H<jats:sub>2</jats:sub>S can be actively synthesized and degraded in the cytosol, chloroplasts, and mitochondria of plant cells by enzymatic and non-enzymatic pathways to maintain homeostasis. To date, plant receptors for H<jats:sub>2</jats:sub>S have not been found. It usually exerts physiological functions through the persulfidation of target proteins. In the past 10 years, H<jats:sub>2</jats:sub>S signaling in plants has gained much attention. Therefore, in this review, based on that same attention, H<jats:sub>2</jats:sub>S homeostasis, protein persulfidation, and the signaling role of H<jats:sub>2</jats:sub>S in plant response to HT and LT stress were summarized. Also, the common mechanisms of H<jats:sub>2</jats:sub>S-induced HT and LT tolerance in plants were updated. These mechanisms involve restoration of biomembrane integrity, synthesis of stress proteins, enhancement of the antioxidant system and methylglyoxal (MG) detoxification system, improvement of the water homeostasis system, and reestablishment of Ca<jats:sup>2+</jats:sup> homeostasis and acid-base balance. These updates lay the foundation for further understanding the physiological functions of H<jats:sub>2</jats:sub>S and acquiring temperature-stress-resistant crops to develop sustainable food and agriculture.</jats:p>

<jats:p>The interactions between plants, beneficial bacteria and their environment are profoundly shaped by various environmental factors, including light, temperature, water availability, and soil quality. Despite efforts to elucidate the molecular mechanisms involved in the association between plants and beneficial bacteria, like Plant Growth-Promoting Bacteria (PGPB), with many studies focusing on the transcriptional reprogramming in the plant, there is no report on the modulation of genetic controls from both plant and associated bacteria standpoints, in response to environment. The main goal of this study was to investigate the relationship between plant-bacteria-environment signaling, using as a model maize plants inoculated with <jats:italic>H. seropedicae</jats:italic> ZAE94 and cultivated with different doses of N (0.3 and 3 mM). For this purpose, we performed rRNA-depleted RNA-seq to determine the global gene expression of both maize roots and associated <jats:italic>H. seropedicae</jats:italic> ZAE94. Our results revealed a differential modulation of maize nitrogen metabolism, phytohormone and cell wall responses when associated with <jats:italic>H. seropedicae</jats:italic> ZAE94 at different N concentrations. In parallel, a modulation of the bacterial metabolism could be observed, by regulating genes involved in transport, secretion system, cell mobility, oxidoreductases, and chemotaxis, when bacteria were associated with maize roots and cultivated at different doses of N. The molecular and phenotypic data of maize plantlets suggested that different doses of N fertilization differentially regulated the beneficial effects of bacterial inoculation, as higher doses (3 mM) favored shoot elongation and lower doses (0.3 mM) favored increase in plant biomass. Our results provide a valuable integrated overview of differentially expressed genes in both maize and associated <jats:italic>H. seropedicae</jats:italic> ZAE94 in response to different N availability, revealing new insights into pathways involved in grass-PGPB associations.</jats:p>

<jats:p>Direct seeding ratoon rice (DSRR) system is a planting method that can significantly increase grain yield, improving light and temperature utilization efficiency and reducing labor input. However, the current nitrogen fertilizer management method which does not aim at the seedling emergence and development characteristics of DSRR just is only based on the traditional method of transplanting ratoon rice, and which is not conducive to the population development and yield improvement. To determine the suitable nitrogen fertilizer application optimization, we set four nitrogen fertilizer application treatments (N0, no nitrogen fertilizer; N1, traditional nitrogen fertilizer; N2, transferring 20% of total nitrogen from basal fertilizer to tillering stage; N3, reducing total nitrogen by 10% from N2 tillering fertilizer) on a hybrid rice “Fengliangyouxiang1 (FLYX1)” and an inbred rice “Huanghuazhan (HHZ)” under DSRR. The effects of treatments on dry matter accumulation, root growth and vigor, leaf area index, leaf senescence rate and yield were investigated. Our results demonstrated that the yield of main crop in N2 treatment was the highest, which was 63.3%, 6.6% and 8.8% higher than that of N0, N1 and N3 treatment, respectively, mainly due to the difference of effective panicle and spikelets number per m<jats:sup>2</jats:sup>. The average of two years and varieties, the annual yield of N2 was significant higher than that of N1 and N3 by 4.94% and 8.55%, respectively. However, there was no significant difference between the annual yields of N1 and N3. N2 treatment had significant effects on the accumulation of aboveground dry matter mass which was no significant difference in 20 days after sowing(DAS), but significant difference in 50 DAS. Meanwhile, the root activity and the leaf senescence rate of N2 treatment was significant lower than that of other treatments. In summary, “20% of total nitrogen was transferred from basal fertilizer to tillering stage” can improve the annual yield and main crop development of DSRR system. Further reducing the use of nitrogen fertilizer may significantly improve the production efficiency of nitrogen fertilizer and improve the planting income in DSRR system.</jats:p>

<jats:p>This study presents a comprehensive analysis of the chloroplast (cp) genomes of <jats:italic>Cornus</jats:italic> species, including comparative and phylogenetic evaluations, as well as examinations of their genomic structure and composition. The cp genomes exhibit a typical circular quadripartite structure and demonstrate highly similar gene order and genomic structure. The complete cp genome size of the 10 taxa in this study is 156,965 bp to 157,383 bp, where the length of the large single-copy (LSC) region is 86,296 bp to 86,691 bp, small single-copy (SSC) region is 18,386 bp to 18,454 bp, and inverted repeat (IR) region is 23,143 bp to 26,112 bp. A total of 131 genes were found, including 86 protein-coding genes (PCGs), eight rRNA genes, and 37 tRNA genes. The mean GC content of the 10 taxa is 38.145%, where the LSC region is 36.396%, the SSC region is 32.372%, and the IR region is 43.076%. Despite the relatively conserved nature of the cp genome within the species of <jats:italic>Cornus</jats:italic>, 25–31 simple sequence repeats (SSRs) were identified in the 10 taxa in our study. The SSRs were found to be distributed in the LSC, SSC, and IR regions in <jats:italic>Cornus hongkongensis</jats:italic> subsp. <jats:italic>hongkongensis</jats:italic>, <jats:italic>C. hongkongensis</jats:italic> subsp. <jats:italic>elegans</jats:italic>, <jats:italic>C. hongkongensis</jats:italic> subsp. <jats:italic>gigantea</jats:italic>, and <jats:italic>C. hongkongensis</jats:italic> subsp. <jats:italic>tonkinensis</jats:italic>, while the SSR was not found in the IR region of the other six taxa. Thus, whole cp genomics is a valuable tool for species identification, taxonomic clarification, and genomic evolutionary analysis. Furthermore, our findings reveal that <jats:italic>C. hongkongensis</jats:italic> and <jats:italic>C. hongkongensis</jats:italic> subsp. <jats:italic>gigantea</jats:italic>, along with <jats:italic>Cornus kousa</jats:italic> and <jats:italic>Cornus elliptica</jats:italic>, form sister groups. Notably, <jats:italic>C. hongkongensis</jats:italic> subsp. <jats:italic>ferruginea</jats:italic> and <jats:italic>C. hongkongensis</jats:italic> subsp. <jats:italic>melanotricha</jats:italic> did not exhibit affinity with <jats:italic>C. hongkongensis</jats:italic> subsp. <jats:italic>hongkongensis</jats:italic>. Our study furnishes essential data for further research on their classification and provides novel insights into the relationship within <jats:italic>Cornus</jats:italic> subg. <jats:italic>Syncarpea</jats:italic>.</jats:p>

<jats:p>Naturally-colored brown cotton (NBC) fiber is an environmentally friendly raw source of fiber for textile applications. The fiber of some NBC cultivars exhibits flame-retardant properties, which can be used in textiles that require flame resistance. Proanthocyanidins or their derivatives are responsible for the brown pigment in NBC; however, how flame retardancy is related to pigmentation in NBC is poorly understood. To gain insight into brown pigment biosynthesis, we conducted comparative transcripts and metabolites profiling analysis of developing cotton fibers between the brown (MC-BL) and white (MC-WL) cotton near-isogenic lines (NILs), genetically different only in the <jats:italic>Lc1</jats:italic> locus. In this study, mass spectrometry was used to detect metabolites in BL and WL developing fibers at 8, 12, 16, 20, 24, 36, and 40 days post anthesis (DPA) and mature fibers. Transcripts analysis was performed at two critical fiber developmental points, 8 DPA (fiber elongation) and 20 DPA (secondary cell wall deposition). We found 5836 (ESI MS positive mode) and 4541 (ESI MS negative mode) metabolites significantly different accumulated between BL and WL. Among them, 142 were known non-redundant metabolites, including organic acids, amino acids, and derivatives of the phenylpropanoid pathway. Transcript analysis determined 1691 (8 DPA) and 5073 (20 DPA) differentially expressed genes (DEGs) between BL and WL, with the majority of DEGs down-regulated at 20 DPA. Organic acids of the citric acid cycle were induced, while most of the detected amino acids were reduced in the MC-BL line. Both <jats:italic>cis</jats:italic>- and <jats:italic>trans</jats:italic>-stereoisomers of flavan-3-ols were detected in developing MC-WL and MC-BL fibers; however, the gallocatechin and catechin accumulated multiple times higher. Gas chromatography-mass spectrometry (GC-MS) analysis of fatty acids determined that palmitic acid long-chain alcohols were the main constituents of waxes of mature fibers. Energy-dispersive X-ray spectrometry (EDS) analysis of mature fibers revealed that potassium accumulated three times greater in MC-BL than in MC-WL mature fibers. This study provides novel insights into the biosynthesis of pigments and its association with flame retardancy in NBC fibers.</jats:p>

<jats:p>Cassava, a vital global food source, faces a threat from Cassava Brown Streak Disease (CBSD). CBSD results from two viruses: Cassava brown streak virus (CBSV) and Ugandan cassava brown streak virus (UCBSV). These viruses frequently pose challenges to the traditional symptom-based 1-5 phenotyping method due to its limitations in terms of accuracy and objectivity. Quantitative polymerase chain reaction (qPCR) offers precise virus quantification, although high costs hinder its widespread adoption. In this research, we utilized qPCR to measure the viral titer/load of CBSV and UCBSV. The objectives were to evaluate titer variability within the Cycle 2 (C2) population in two different environments, establish connections between viral titers and CBSD severity scores from the 1-5 scoring method, perform Genome-Wide Association Studies (GWAS) to identify genomic regions associated with CBSV and UCBSV titers, and investigate the functional annotated genes. The results demonstrated a significantly higher prevalence of CBSV (50.2%) in clones compared to UCBSV (12.9%) with mixed infections in some cases. Genotypic effects, particularly concerning UCBSV, were significant, with genotype-by-environment effects primarily influencing CBSV titer. GWAS Studies identified genomic regions associated with CBSV and UCBSV titers. Twenty-one SNP markers on chromosomes 10, 13, 17, and 18 exhibited significant associations with CBSV titer, collectively explaining 43.14% of the phenotypic variation. Additionally, 25 SNP markers on chromosomes 1, 2, 4, 5, 8, 11, 12, 13, 16, and 18 were associated with UCBSV titer, and explained 70.71% of the phenotypic variation. No shared genomic regions were identified between CBSV and UCBSV viral titers. Gene ontology analysis also revealed diverse gene functions, especially in transport and catalytic activities. These findings enhance our understanding of virus prevalence, genetics, and molecular functions in cassava plants, offering valuable insights for targeted breeding strategies.</jats:p>