Kernel rate (KR), the ratio of kernel to ear weight, serves as a key metric of assimilate partitioning efficiency and determines single-ear yield stability under high planting densities. Despite its critical role in modern intensive agriculture, the genetic architecture of KR remains largely elusive. Here, we performed a genome-wide association study (GWAS) for KR and its component traits—ear weight (EW), kernel weight (KW), and cob weight (CW)—using a diverse panel of 502 maize inbred lines across seven environments. Phenotypic profiling revealed substantial variation and high heritability. Leveraging 10.77 million high-quality SNPs, we identified 202 significant associations, which were refined into 106 quantitative trait loci (QTL), each explaining 5

Background: Ideal plant architecture is central to high-yield maize breeding. The proportional length of internodes above the ear plays a crucial role in determining plant architecture. Methods: In this study, we used an association panel comprising 288 maize inbred lines and performed genome-wide association studies (GWASs) with 1.25 M high-density single nucleotide polymorphism (SNP) markers under a Q + K mixed linear model. Results: A total of 821 significant SNPs associated with plant height (PH), height above ear (HAE), and internode-related traits were detected, which were further classified into 417 quantitative trait loci (QTL). Among these, 128 significant SNPs and 44 QTL were identified for the U1/HAE trait, and 37 significant SNPs and 27 QTL for the U1/PH trait. Four stable QTL (qU1-qU4) were identified through colocalization analysis. Two candidate genes, Zm00001d013222 (involved in gibberellin signaling) and Zm00001d021304 (involved in cell wall metabolism), were further supported by haplotype analysis. For the former gene, U1/PH values in Hap1 and Hap3 were significantly lower than those in Hap2 (p < 0.01). For the latter gene, Hap2 exhibited a significantly higher U1/HAE value compared to Hap1 (p < 0.001). Conclusions: These findings provide new genetic insights into the regulation of maize internode proportion and plant architecture, offering potential targets for molecular breeding.

This study examines the impact of Holstein dry cows' prenatal heat tolerance (n = 180) on their calves' thermoregulation and immunity. Holstein cows (body condition score 3.29 +/- 0.39, parity 2.64 +/- 0.79) were monitored for body temperature (BT), respiratory rate (RR), and microenvironmental temperature and humidity twice daily for seven days during heat stress. Mixed-effects model and cluster method identified heat-tolerant (n = 68) and heat-sensitive (n = 114) dry cows. Once cows gave birth, the RR and BT of 2-day-old calves were recorded every 2 h for two days, totaling five measurements per day, to assess thermoregulatory responses using generalized linear mixed models. Calves in the heat-tolerant group had a better thermoregulatory response than the heat-sensitive group, RR of heat-tolerant calves was significantly higher than the heat-sensitive calves (P = 0.02). Plasma indicators were analyzed to assess calf immunity. Heat-tolerant calves had significantly lower plasma cortisol, tumor necrosis factor-alpha, interleukin 2, interleukin 4, interleukin 6, and interleukin 10 concentrations compared to heat-sensitive calves (P < 0.05). In both cows and calves, plasma cortisol concentrations in the heat-tolerant groups were lower than those in heat-sensitive groups. In comparison, plasma heat shock protein 70 and heat shock protein 90 concentrations were higher (P < 0.05). In conclusion, calves born to heat-tolerant cows had higher thermoregulation and immunity than calves born to heat-sensitive cows when exposed to heat stress.

Protein content (PC) in maize kernels is a key determinant of their nutritional quality, however, its genetic basis remains largely unexplored. In this study, we conducted a genome-wide association study (GWAS) using 264 maize inbred lines and 1.25 million single nucleotide polymorphisms (SNPs), applying six GWAS models: BLINK, FarmCPU, MLM, MLMM, SUPER, and 3VmrMLM. Kernel PC exhibited substantial variation, ranging from 9.26 to 20.94%, with a broad-sense heritability of 0.56. A total of 473 significant quantitative trait nucleotides (QTNs) were detected, each explaining 0.08 to 7.10% of the phenotypic variance. Among them, 115 QTNs were consistently detected across different models, environments and analytical methods. Notably, 3VmrMLM model identified 59 most significant QTNs, with 38 were QEIs, and the MLM model identified the fewest significant QTNs (8). We further identified 35 candidate genes located within or adjacent to the significant QTNs. Among these, four genes - Zm00001d033805, Zm00001d037565, Zm00001d052164 and Zm00001d031535 - were strongly associated with PC. These genes are implicated in critical biological pathways, including nitrogen metabolism, photosynthesis, and the tricarboxylic acid (TCA) cycle. Notably, Zm00001d037565, encoding a gibberellin 2-oxidase, plays a role in seed development and is likely involved in regulating protein accumulation in kernels. Haplotype analysis revealed that the HapA of Zm00001d037565 is significantly associated with higher PC. Selective sweep analysis indicated that this gene underwent selection during maize domestication from teosinte (Zea mays ssp. mexicana and Zea mays ssp. parviglumis), its adaptation from tropical/subtropical to temperate regions, and throughout modern breeding programs. Overall, this study advances our understanding of the genetic architecture of maize kernel PC and provides valuable candidate genes and haplotypes for marker-assisted selection, offering new targets for developing high-protein maize varieties.

OBJECTIVE:To investigate the molecular mechanisms underlying EA(elaidic acid)-induced lipid accumulation in VSMCs(vascular smooth muscle cells). METHODS:CCK-8 assay determined the effects of EA(0-2.8 mmol/L) on MOVAS(murine aortic vascular smooth muscle cells)to select experimental concentrations. Oil Red O staining combined with quantitative lipid droplet analysis was conducted to examine the effects of EA on intracellular lipid droplet accumulation. Intracellular total cholesterol(TC) and triglyceride(TG) levels were quantified spectrophotometrically to assess EA&apos;s effects on intracellular lipid levels. Western blot analyzed protein expression of PPARγ, LXRα, ABCA1, and ABCG1 to delineate EA&apos;s pro-foamogenic mechanism. RESULTS:EA dose-dependently suppressed MOVAS viability(P&lt;0.01). EA-treated groups exhibited significant increases in lipid droplet area/number and TC/TG content versus controls(P&lt;0.01). EA downregulated PPARγ and LXRα protein expression(P&lt;0.05), subsequently suppressing downstream targets ABCA1 and ABCG1(P&lt;0.05). CONCLUSION:EA disrupts lipid metabolism in VSMCs by inhibiting the PPARγ-LXRα-ABCA1/ABCG1 signaling pathway, thereby inducing lipid accumulation and promoting foam cell formation.

Hybridization has long been a crucial strategy for breeders aiming to develop high-yield crops vital for global food security. However, the exact molecular mechanisms driving heterosis (hybrid vigor) remain a topic of debate. Maize (Zea mays), which demonstrates pronounced heterosis, serves as an ideal model for studying this phenomenon. In our study, we carefully measured phenotypic changes in ear diameter, tracing its development from the inflorescence meristem (IM) to the floral meristem (FM) stages. Our findings revealed a complex progression: the hybrid's ear diameter followed an additive pattern during the IM and spikelet pair meristem (SPM) stages, shifted to incomplete dominance at the spikelet meristem (SM) stage, and ultimately displayed over-dominance at the FM stage. Notably, significant phenotypic changes occurred during the SM stage with gene expression primarily showing non-additive patterns. Gene Ontology (GO) enrichment analysis highlighted the role of cell redox homeostasis genes, which exhibited over-dominant expression in hybrids, as key contributors to heterosis. Furthermore, we identified a distinct gene expression category - dominant maternal or paternal gene expression in F1 hybrids (DMP) - characterized by exclusive expression in the hybrid and one parent, while remaining inactive in the other. This category of DMP genes plays a pivotal role in shaping the diverse gene expression patterns observed in hybrids, distinguishing them from their parental lines. In conclusion, the widespread occurrence of non-additive expression seems to enhance the efficiency of biological processes and energy distribution in hybrids, ultimately driving the manifestation of heterosis.

In summary, we characterized a maize semi-dwarf mutant, sdw9, and successfully isolated the responsible gene, which encodes a GRAS protein, through a combination of map-based cloning and Re-sequencing (Re-seq). Our findings demonstrate that the candidate gene ZmGRAS42 regulates BR signaling genes, thereby influencing internode development. This regulatory function likely involves processes such as cell division, cell cycle regulation and cell wall synthesis. Favorable variations of ZmGRAS42 identified in this study may hold promise for the development of lodging-resistant maize cultivars suitable for high-density planting, contributing to the improvement of maize breeding programs. Plant height and lateral root angle are crucial determinants of plant architecture in maize (Zea mays) which are closely related to lodging resistance at high planting density. These traits are intricately regulated by various phytohormones. Mutations affecting hormone biosynthesis and signaling often lead to reduced yield alongside diminished plant height, posing challenges in breeding dwarf maize varieties. In this study, the maize mutant sdw9 was characterized, which displays shorter stature and altered lateral root angle compared to WT, while showing potential to increase planting density and improve overall yield despite a slight reduction in single-ear yield. Employing positional cloning coupled with Re-seq techniques, we pinpointed a transposon insertion in the candidate gene ZmGRAS42, which encodes a GRAS transcription factor involved in BR signaling in maize. Transcriptome analysis revealed that ZmGRAS42 orchestrates the expression of several known dwarfing genes such as D8, Br2, and Na2, along with genes associated with cell wall organization, cell division, and cell cycle regulation, notably Cesa4, Cesa7, and Cyc11. Furthermore, identification of favorable ZmGRAS42 haplotypes linked to reduced plant height offers novel avenues for maize breeding strategies. These findings not only hold the potential for enhancing maize lodging resistance but also for optimizing land utilization through high-density planting practices.

The full text of this preprint has been withdrawn by the authors while they make corrections to the work. Therefore, the authors do not wish this work to be cited as a reference. Questions should be directed to the corresponding author.

This study was to evaluate the effect of supplementing the diet of broilers with Neolamarckia cadamba leaf extract (NCLE) on meat quality by evaluating antioxidant parameters and the expression of genes in the p38 mitogen-activated protein kinase/nuclear factor-erythroid 2-related factor 2/antioxidant responsive element (p38 MAPK/Nrf2/ARE) signaling pathway, coupled with LC-MS-based metabolomic analysis. A total of 480 one-day-old male broilers were randomly allocated to four treatment groups-a control (CON) group, which was fed a basal diet, and three NCLE treatment groups, which were fed the basal diet supplemented with 100, 200, or 400 mg/kg NCLE (N1, N2, and N3 groups, respectively) for 42 d. Compared with the CON group, meat quality was improved in the N2 and N3 groups, as evidenced by the higher pH45min (P < 0.05) and lower shear force (P < 0.05) in breast muscle (BM) and lower drip loss at 48 h (P < 0.05) in leg muscle (LM). Moreover, BM antioxidant capacity was significantly enhanced in the N3 group, characterized by an increase in the total antioxidant capacity (T-AOC), the concentrations of glutathione peroxidase (GSH-Px) and catalase (CAT), and the relative mRNA expression of p38 MAPK, extracellular-signal regulated kinase (ERK1/2), c-Jun N-terminal kinase (JNK), Nrf2, CAT, and GSH-Px (P < 0.05). Similarly, LM in the N3 group displayed higher T-AOC, increased GSH-Px and CAT concentrations, reduced malonaldehyde contents (P < 0.05), and upregulation of the relative mRNA levels of JNK, Nrf2, heme oxygenase, CAT, and superoxide dismutase (SOD) (P < 0.05). Metabolomics analysis revealed that D-arabinono-1,4-lactone and lyso-PAF C-16-d4 were negatively correlated with shear force and cooking loss (P < 0.05) and displayed increased abundance in BM of the N3 group. L-Serine levels were upregulated while D-fructose 1,6-diphosphate contents were downregulated in the three NCLE groups. Finally, the differential metabolites in both BM and LM were involved in amino acid metabolism pathways. Our results indicated that NCLE supplementation improved meat quality by enhancing antioxidant enzyme activities, promoting the expression of genes in the p38 MAPK/Nrf2/ARE signaling pathway, and regulating amino acid metabolism. The optimal NCLE concentration was found to be 400 mg/kg.

ABSTRACT The effects of Neolamarckia cadamba leaves extract (NCLE), with effective ingredients of flavonoids, on antibiotic resistance genes (ARGs) and relevant microorganisms in cecal contents and feces of broilers treated with or without lipopolysaccharide stimulation (LPS) were investigated. LPS stimulation increased ( P < 0.05) the relative abundance of ARGs and mobile genetic elements (MGEs), such as tet(W/N/W ), APH(3')-IIIa , ErmB , tet (44 ), ANT (6)-Ia , tet(O ), tet (32 ), Vang_ACT_CHL , myrA , ANT (6)-Ib , IncQ1 , tniB , and rep2 in cecal contents. However, the difference disappeared ( P > 0.05) when NCLE was added at the same time. These differential ARGs and MGEs were mainly correlated ( P < 0.01) with Clostridiales bacterium, Lachnospiraceae bacterium, and Candidatus Woodwardibium gallinarum . These species increased in LPS-stimulated broilers and decreased when NCLE was applied at the same time. In feces, LPS stimulation decreased ( P < 0.05) the relative abundance of tet(Q ), adeF , ErmF , Mef(En2 ), OXA-347 , tet (40 ), npmA , tmrB, CfxA3, and ISCrsp1, while the LPS + NCLE treated group showed no significant effect ( P > 0.05) on these ARGs. These differential ARGs and MGEs in feces were mainly correlated ( P < 0.01) with Clostridiales bacterium, Pseudoflavonifractor sp . An184, Flavonifractor sp . An10, Ruminococcaceae bacterium, etc. These species increased in LPS-stimulated broilers and increased when NCLE was applied at the same time. In conclusion, LPS stimulation and NCLE influenced microbial communities and associated ARGs in both cecal contents and feces of broilers. NCLE alleviated the change of ARGs and MGEs in LPS-induced broilers by maintaining the microbial balance. IMPORTANCE Antibiotics showed a positive effect on gut health regulation and growth performance improvement in livestock breeding, but the antimicrobial resistance threat and environment pollution problem are increasingly severe with antibiotics abuse. As alternatives, plant extract containing bioactive substances are increasingly used to improve immunity and promote productivity. However, little is known about their effects on diversity and abundance of ARGs. Here, we investigated the effects of NCLE, with effective ingredients of flavonoids, on ARGs and relevant microorganisms in cecal contents and feces of broilers treated with or without lipopolysaccharide stimulation. We found that NCLE reduced the abundance of ARGs in cecal contents of lipopolysaccharide-induced broilers by maintaining the microbial balance. This study provides a comprehensive view of cecal and fecal microbial community, ARGs, and MGEs of broiler following LPS stimulation and NCLE treatment. It might be used to understand and control ARGs dissemination in livestock production.

Maize tassel spindle length is closely related to the number of pollen grains and the duration of the flowering stage, ultimately affecting maize yield and adaptations to stress conditions. In this study, 182 maize inbred lines were included in an association population. A genome-wide association study was conducted on maize tassel spindle length using the Q + K model. With p ≤ 1.0 × 10−4 applied as the significance threshold, 240 SNPs significantly associated with tassel spindle length were detected, which were associated with 99 quantitative trait loci (QTLs), with 21 QTLs detected in two or more environments. Moreover, 51 candidate genes were detected in 21 co-localized QTLs. A KEGG enrichment analysis and candidate gene expression analysis indicated that Zm00001d042312 affects plant hormone signal transduction and is highly expressed in maize tassels. A haplotype analysis of Zm00001d042312 revealed three main haplotypes, with significant differences between Hap1 and Hap2. In conclusion, we propose that Zm00001d042312 is a gene that regulates maize tassel spindle length. This study has further elucidated the genetic basis of maize tassel spindle length, while also providing excellent genetic targets and germplasm resources for the genetic improvement of maize tassel spindle length and yield.

Embryogenic callus (EC) has strong regenerative potential, useful for propagation and genetic transformation. miRNAs have been confirmed to play key regulatory roles in EC regeneration across various plants. However, challenges in EC induction have hindered the breeding of drumstick (Moringa oleifera Lam.), a tree with significant commercial potential. Understanding the regulatory networks of miRNAs-lncRNAs during EC formation in drumstick is crucial for overcoming these barriers. In this study, three drumstick EC small RNA libraries were sequenced using an Illumina Nova 6000 system. We identified 50 known miRNAs and 233 novel miRNAs. Target prediction and functional analysis showed that these miRNAs are involved in plant hormone signal transduction. Notably, miR319a and miR319b were upregulated throughout the entire process, while miR171 and miR160 were downregulated in the earlier stage but upregulated in the later stage. The expression patterns of 6 miRNAs detected by qRT-PCR were consistent with those observed in RNA-seq. The regulatory relationships between 6 selected highly expressed miRNAs and their target genes generally conformed to a negative regulatory pattern. Furthermore, miR156 and MolncRNA2275 were identified as key regulators in miRNA-mRNA-lncRNA network. In summary, our study provides valuable insights into the molecular mechanisms underlying EC formation and enhances the understanding of the miRNA networks involved in this process.

This study uncovers the role of H4K8hib as an active epigenetic mark in rice that positively correlates with gene expression and enhances immune responses. Furthermore, HDA705 was identified as the key enzyme regulating H4K8hib. Mutation of HDA705 led to hyper-H4K8hib, which in turn activated the expression of defense-related genes and enhanced rice resistance to pathogens.

Maize ( Zea mays ) represents one of the most successful uses of heterosis among crops. Hybrid maize seeds can be produced by crossing a male-sterile female parent with a male parent as the pollen donor to achieve high seed purity at low cost. Cytoplasmic male sterility (CMS) has been widely used for maize hybrid seed production. Recently, several hybrid seed production technologies based on genic male sterility (GMS) genes have been developed. In addition, the identification of environment-sensitive genic male sterility (EGMS) genes provides opportunities for the two-line system to be applied in maize hybrid seed production. In this review, we systematically summarize the male-sterile genes and molecular mechanisms of male sterility in maize. Future prospects for the study of maize male sterility are highlighted. Future research will enhance our understanding of the molecular regulatory networks of male sterility and promote the process of maize hybrid seed production using male sterile lines.

Neolamarckia cadamba (N. cadamba) is an evergreen tree species known for its rapid growth, remarkable wood properties, and significant value in medicine, feeding, and landscape. In order to clone a N. cadamba individual with excellent genotype, a plant regeneration protocol was successfully established with leaves wrapped by bud scales as explants. The optimal sterilization method for the leaves was 0.1

Silage, an anaerobic fermented feed for animals, is subjected to aerobic deterioration easily due to the activities of undesirable microorganisms. Aerobic deterioration always leads to the reduction of important nutritional components, animal performance and food safety. To better understand aerobic deterioration and the underlying mechanisms of Neolamarckia cadamba leaves (NCL) essential oil, metagenomic, metatranscriptomic, and metabolome analyses of silage and antimicrobial activity of NCL essential oil were performed. During exposure to air, whole-crop corn silage deteriorated as the temperature, pH value, yeasts and molds counts increased (p < 0.001), while lactic acid, acetic acid contents decreased (p < 0.001). Bacillales, Clostridiales, Saccharomycetales, and Eurotiales were active, which might be responsible for the aerobic deterioration of silage and the change in metabolites. NCL essential oil showed strong antibacterial ability to strains isolated from aerobically deteriorated silage including Candida glabrata, and Niallia circulans by affecting metabolism pathways. The addition of NCL essential oil increased the aerobic stability of whole-crop corn silage by preventing the decrease of acids and increase of temperature, pH value, yeasts and molds counts, and the relative abundances of Eurotiales, Saccharomycetales, Bacillales, and Eubacteriales. Genes related to metabolism including amino acid metabolism were down-regulated in NCL essential oil treatment. Differentially accumulated metabolites annotation indicated that pathways related to metabolism, especially amino acid metabolism were enriched. In summary, NCL essential oil could improve the aerobic stability of whole-crop corn silage by inhibiting metabolism activities, especially the amino acid metabolism of aerobic deterioration sponsors such as Saccharomycetales and Bacillales. This study provides deeper insight, a new target for controlling aerobic deterioration, and a theoretical basis for high-quality silage production.

Toona ciliata is an important timber species but is recognized as an endangered species at level II in China. Its genetic conservation is of increasing concern. Provenance trials and other breeding programs were conducted to develop seed transfer rules and multiplications. Here, we investigated twenty-nine populations sampled across the natural distribution of the T. ciliata complex using mtDNA and nrDNA ITS (ribosomal internal transcribed spacer) markers. Haplotype diversity was h = 0.190 ± 0.202 and nucleotide diversity was π = 0.000383 ± 0.000536 for mtDNA marker. Nucleotide diversity for ITS sequences was 0.00837 ± 0.000783. Haplotypes exhibited phylogeographic structure in spatial distribution. The extent of genetic differentiation was significant (Fst = 0.6994 ± 0.0079 for ITS and 0.8870 ± 0.0077 for mtDNA marker). Isolation by distance (IBD) and by elevation (IBE) occurred among populations. Phylogenetic relationships from mtDNA marker indicated three genetically distinct regions, each without IBD effects. Compared with pollen flow, seed flow was strongly impeded in the western region, but extensive in the central region, and less impeded in the eastern region. Most populations did not exhibit expansion, with only a few populations showing expansion after bottleneck effects. We discussed a strategy of region-based genetic conservation and proposed to conserve multiple populations in the western and eastern regions and a few populations in the central region.

In order to explore the germplasm resources of male sterile line and identify the male fertility genes, which would provide the basic materials for the maize seed production by the male sterile line. Using the male sterile mutant x50 as the experimental material, the male sterile phenotype of x50 was studied, and the F 1 and F 2 populations of x50 and inbred line Mo17 were constructed to determine the genetic pattern of the male sterile trait in x50.With the F 2 population, the male fertility gene X50 was identified by the map-based cloning.Furthermore, the candidate gene was confirmed by the allelism test.The results showed that compared with the wild type, the x50 anthers did not emerge from the glume, and was smaller and wilted, and no mature pollen grains were formed.All F 1 plants were fertile, and F 2 plants displayed 3∶1 segregation ratio between fertile and sterile plants, indicating that the monofactorial recessive inheritance of x50.The gene X50 was mapped to the interval from the molecular marker 2-4901 to 2-4963 on chromosome 2 with a physical range of 237.42 to 241.39 Mb by map-based cloning.Candidate gene analysis found that the male fertility gene ZmMs33 was located in the mapping region.In addition, the test crosses of the ms33 mutants（ms33-6029 and ms33-6052）and heterozygous +/x50 revealed 1∶1 segregation ratio between fertile and sterile plants.These results suggested that x50 was an allele mutant of ZmMs33 gene.The identification of the male sterile mutant x50 provided germplasm resources for maize hybrid seed production and functional study of ZmMs33 gene.

Neolamarckia cadamba is an evergreen tree species growing fast, with not only good wood properties, but also great value in medicine, feeding and landscape. In order to clone an excellent genotype individual of N. cadamba, the plant regeneration protocol was successfully established with leaves wrapped by bud scales in the wild as explants. The optimal sterilization method for the leaves was 0.1% HgCl2 treatment for 1 min before culturing on Murashige and Skoog’s (MS) medium supplemented with 3.0 mg/L thidiazuron (TDZ), 0.1 mg/L 2–4 dichlorophenoxyacetic acid (2-4D) and 0.05 mg/L α-naphthaleneacetic (NAA) acid to induce calluses. Additionally, the medium supplemented with 1 mL/L PPM could effectively inhibit the medium contamination without an unfavorable influence on the final induction rate of calluses from the leaves. Three types of calluses were induced from the leaves cultured on the above medium. Among them, only the emerald callus with bud points on its surface could differentiate into adventitious shoots on the MS medium supplemented with 1.5 mg/L 6–benzylaminopurine (6-BA) and 0.05 mg/L NAA, with the induction rate of 78.89%. The adventitious shoots were proliferated on the MS medium supplemented with 1.0 mg/L 6-BA and 0.05 mg/L indole-3- butyric acid (IBA). And the micro-shoots developed roots in the MS medium supplemented with 0.05 mg/L NAA and 0.05 mg/L IBA. The regeneration protocol can be used in the propagation and large scale production of seedlings with the same genotype as an excellent individual of N. cadamba in the wild.