The identification and expression pattern of the sex determination genes and their sex-specific variants in the egg parasitoid Trichogramma dendrolimi Matsumura (Hymenoptera: Trichogrammatidae)

Introduction: Trichogramma wasps are egg parasitoids of agricultural lepidopteran pests. The sex of Trichogramma is determined by its ploidy as well as certain sex ratio distorters, such as the endosymbiotic bacteria Wolbachia spp. and the paternal sex ratio (PSR) chromosome. The sex determination systems of hymenopterans, such as Trichogramma spp., involve cascades of the genes transformer (tra), transformer-2 (tra2), and doublesex (dsx) and are associated with sex-specific tra and dsx splicing. First, these genes and their sex-specific variants must be identified to elucidate the interactions between the sex ratio disorders and the sex determination mechanism of Trichogramma. Methods: Here, we characterized the sex determination genes tra, tra2, and dsx in Trichogramma dendrolimi. Sex-specific tra and dsx variants were detected in cDNA samples obtained from both male and female Trichogramma wasps. They were observed in the early embryos (1-10 h), late embryos (12-20 h), larvae (32 h and 48 h), pre-pupae (96 h), and pupae (144 h, 168 h, 192 h, and 216 h) of both male and female T. dendrolimi offspring. Results: We detected female-specific tra variants throughout the entire early female offspring stage. The male-specific variant began to express at 9-10 h as the egg was not fertilized. However, we did not find any maternally derived, female-specific tra variant in the early male embryo. This observation suggests that the female-specific tra variant expressed in the female embryo at 1-9 h may not have originated from the maternal female wasp. Discussion: The present study might be the first to identify the sex determination genes and sex-specific gene splicing in Trichogramma wasps. The findings of this study lay the foundation for investigating the sex determination mechanisms of Trichogramma and other wasps. They also facilitate sex identification in immature T. dendrolimi and the application of this important egg parasitoid in biological insect pest control programs.

Untargeted metabolomics reveal rhizosphere metabolites mechanisms on continuous ramie cropping

Ramie is an important fiber feed dual-purpose crop in China and plays an important role in the national economy. However, ramie yield and quality can be reduced after many years of continuous cultivation. Currently, relatively little research has been conducted on rhizosphere metabolites and their pathways in continuous ramie cropping. Therefore, a healthy group (CK) and obstacle groups (XZQG, JZ, DJY, and GXD) with 8 years of continuous cultivation were selected for the study. LC-MS and GC-MS untargeted metabolomics were used to explore and analyze ramie rhizosphere metabolites and pathways. The results revealed that significant differences in the agronomic traits of ramie occurred after 8 years of continuous cultivation, with dwarfed plants and decreased yields in the obstacle groups. Metabolomic analysis identified 49 and 19 rhizosphere metabolites, including lipids, organic acids, phenols, and amino acids. In addition, four differential metabolic pathways (phenylpropanoid biosynthesis, fatty acid metabolism, amino acid metabolism, and ascorbate and aldarate metabolism) were elucidated. It was also clarified that sinapic acid, jasmonic acid, glutamine, and inositol might be the main metabolites affecting ramie continuous-cropping obstacle groups, and they were significantly correlated with ramie agronomic traits and physiological indicators. This provided important insights into the mechanisms affecting continuous ramie cropping. Accordingly, it is expected that the increase or decrease of sinapic acid, jasmonic acid, glutamine, and inositol in the soil will alleviate obstacles to continuous ramie cropping and promote the healthy development of the ramie industry in the future.

Argonaute 1 and 5 proteins play crucial roles in the defence against cucumber green mottle mosaic virus in watermelon

RNA silencing, a core part of plants' antiviral defence, requires the ARGONAUTE, DICER-like, and RNA-dependent RNA polymerase proteins. However, how these proteins contribute to watermelon's RNA interference (RNAi) pathway response to cucumber green mottle mosaic virus (CGMMV) has not been characterized. Here, we identify seven ClAGO, four ClDCL, and 11 ClRDR genes in watermelon and analyse their expression profiles when infected with CGMMV. ClAGO1 and ClAGO5 expression levels were highly induced by CGMMV infection. The results of ClAGO1 and ClAGO5 overexpression and silencing experiments suggest that these genes play central roles in watermelon's antiviral defence. Furthermore, co-immunoprecipitation and bimolecular fluorescence complementation experiments showed that ClAGO1 interacts with ClAGO5 in vivo, suggesting that ClAGO1 and ClAGO5 co-regulate watermelon defence against CGMMV infection. We also identified the ethylene response factor (ERF) binding site in the promoters of the ClAGO1 and ClAGO5 genes, and ethylene (ETH) treatment significantly increased ClAGO5 expression. Two ERF genes (Cla97C08G147180 and Cla97C06G122830) closely related to ClAGO5 expression were identified using co-expression analysis. Subcellular localization revealed that two ERFs and ClAGO5 predominantly localize at the nucleus, suggesting that enhancement of resistance to CGMMV by ETH is probably achieved through ClAGO5 but not ClAGO1. Our findings reveal aspects of the mechanisms underlying RNA silencing in watermelon against CGMMV.

Determination of optimal NH4+/K + concentration and corresponding ratio critical for growth of tobacco seedlings in a hydroponic system

Inherently, ammonium (NH₄ ⁺) is critical for plant growth; however, its toxicity suppresses potassium (K⁺) uptake and vice-versa. Hence, attaining a nutritional balance between these two ions (NH₄ ⁺ and K⁺) becomes imperative for the growth of tobacco seedlings. Therefore, we conducted a 15-day experimental study on tobacco seedlings exposed to different concentrations (47 treatments) of NH₄ ⁺/K⁺ at different corresponding 12 ratios simultaneously in a hydroponic system. Our study aimed at establishing the optimal NH₄ ⁺-K⁺ concentration and the corresponding ratio required for optimal growth of different tobacco plant organs during the seedling stage. The controls were the baseline for comparison in this study. Plants with low or excessive NH₄ ⁺-K⁺ concentration had leaf chlorosis or dark greenish colouration, stunted whole plant part biomass, and thin roots. We found that adequate K⁺ supply is a pragmatic way to mitigate NH₄ ⁺-induced toxicity in tobacco plants. The optimal growth for tobacco leaf and root was attained at NH₄ ⁺-K⁺ concentrations 2-2 mM (ratio 1:1), whereas stem growth was optimal at NH₄ ⁺-K⁺ 1-2 mM (1:2). The study provided an insight into the right combination of NH₄ ⁺/K⁺ that could mitigate or prevent NH₄ ⁺ or K⁺ stress in the tobacco seedlings.

Posterior concentration of Wolbachia during the early embryogenesis of the host dynamically shapes the tissue tropism of Wolbachia in host Trichogramma wasps

Introduction

The bacterial endosymbiont, Wolbachia spp. induce thelytokous parthenogenesis in certain parasitoid wasps, such as the egg parasitoid wasps Trichogramma spp. To complete the cycle of vertical transmission, Wolbachia displays efficient transovarial transmission by targeting the reproductive tissues and often exhibits strong tissue-specific tropism in their host.

Method

The present study aimed to describe the basic Wolbachia distribution patterns that occur during the development of Wolbachia-infected, thelytokous Trichogramma dendrolimi, and T. pretiosum. We used fluorescence in situ hybridization (FISH) to investigate Wolbachia signal dynamics during early embryogenesis (from 30 to 120 min). Wolbachia titers and distributions from the embryo to adult stages of Trichogramma after early embryogenesis were detected by absolute quantitative polymerase chain reaction (AQ-PCR) and FISH. The symmetry ratios (SR) of the Wolbachia signals were calculated using the SR odds ratios in the anterior and posterior parts of the host. The SR was determined to describe Wolbachia tropism during early embryogenesis and various developmental stages of Trichogramma.

Results

Wolbachia was concentrated in the posterior part of the embryo during early embryogenesis and the various developmental stages of both T. dendrolimi and T. pretiosum. Wolbachia density increased with the number of nuclei and the initial mitotic division frequency during early embryogenesis. The total Wolbachia titer increased with postembryogenesis development in both T. dendrolimi and T. pretiosum. However, the Wolbachia densities relative to body size were significantly lower at the adult and pupal stages than they were at the embryonic stage.

Discussion

The present work revealed that posterior Wolbachia concentration during early host embryogenesis determined Wolbachia localization in adult wasps. By this mechanism, Wolbachia exhibits efficient vertical transmission across generations by depositing only female Wolbachia-infected offspring. The results of this study describe the dynamics of Wolbachia during the development of their Trichogramma host. The findings of this investigation helped clarify Wolbachia tropism in Trichogramma wasps.

Comparative physiological, metabolomic, and transcriptomic analyses reveal mechanisms of apple dwarfing rootstock root morphogenesis under nitrogen and/or phosphorus deficient conditions

Nitrogen (N) and phosphorus (P) are essential phytomacronutrients, and deficiencies in these two elements limit growth and yield in apple (Malus domestica Borkh.). The rootstock plays a key role in the nutrient uptake and environmental adaptation of apple. The objective of this study was to investigate the effects of N and/or P deficiency on hydroponically-grown dwarfing rootstock 'M9-T337' seedlings, particularly the roots, by performing an integrated physiological, transcriptomics-, and metabolomics-based analyses. Compared to N and P sufficiency, N and/or P deficiency inhibited aboveground growth, increased the partitioning of total N and total P in roots, enhanced the total number of tips, length, volume, and surface area of roots, and improved the root-to-shoot ratio. P and/or N deficiency inhibited NO3 - influx into roots, and H⁺ pumps played a important role in the response to P and/or N deficiency. Conjoint analysis of differentially expressed genes and differentially accumulated metabolites in roots revealed that N and/or P deficiency altered the biosynthesis of cell wall components such as cellulose, hemicellulose, lignin, and pectin. The expression of MdEXPA4 and MdEXLB1, two cell wall expansin genes, were shown to be induced by N and/or P deficiency. Overexpression of MdEXPA4 enhanced root development and improved tolerance to N and/or P deficiency in transgenic Arabidopsis thaliana plants. In addition, overexpression of MdEXLB1 in transgenic Solanum lycopersicum seedlings increased the root surface area and promoted acquisition of N and P, thereby facilitating plant growth and adaptation to N and/or P deficiency. Collectively, these results provided a reference for improving root architecture in dwarfing rootstock and furthering our understanding of integration between N and P signaling pathways.

Molecular epidemiology and characterization of antimicrobial-resistant Staphylococcus haemolyticus strains isolated from dairy cattle milk in Northwest, China

Introduction

Non-aureus Staphylococcus (NAS) species are currently the most commonly identified microbial agents causing sub-clinical infections of the udder and are also deemed as opportunistic pathogens of clinical mastitis in dairy cattle. More than 10 NAS species have been identified and studied but little is known about S. haemolyticus in accordance with dairy mastitis. The present study focused on the molecular epidemiology and genotypic characterization of S. haemolyticus isolated from dairy cattle milk in Northwest, China.

Methods

In this study, a total of 356 milk samples were collected from large dairy farms in three provinces in Northwest, China. The bacterial isolation and presumptive identification were done by microbiological and biochemical methods following the molecular confirmation by 16S rRNA gene sequencing. The antimicrobial susceptibility testing (AST) was done by Kirby-Bauer disk diffusion assay and antibiotic-resistance genes (ARGs) were identified by PCR. The phylogenetic grouping and sequence typing was done by Pulsed Field Gel Electrophoresis (PFGE) and Multi-Locus Sequence Typing (MLST) respectively.

Results

In total, 39/356 (11.0%) were identified as positive for S. haemolyticus. The overall prevalence of other Staphylococcus species was noted to be 39.6% (141/356), while the species distribution was as follows: S. aureus 14.9%, S. sciuri 10.4%, S. saprophyticus 7.6%, S. chromogenes 4.2%, S. simulans 1.4%, and S. epidermidis 1.1%. The antimicrobial susceptibility of 39 S. haemolyticus strains exhibited higher resistance to erythromycin (92.3%) followed by trimethoprim-sulfamethoxazole (51.3%), ciprofloxacin (43.6%), florfenicol (30.8%), cefoxitin (28.2%), and gentamicin (23.1%). All of the S. haemolyticus strains were susceptible to tetracycline, vancomycin, and linezolid. The overall percentage of multi-drug resistant (MDR) S. haemolyticus strains was noted to be 46.15% (18/39). Among ARGs, mphC was identified as predominant (82.05%), followed by ermB (33.33%), floR (30.77%), gyrA (30.77%), sul1 (28.21%), ermA (23.08%), aadD (12.82%), grlA (12.82%), aacA-aphD (10.26%), sul2 (10.26%), dfrA (7.69%), and dfrG (5.13%). The PFGE categorized 39 S. haemolyticus strains into A-H phylogenetic groups while the MLST categorized strains into eight STs with ST8 being the most predominant while other STs identified were ST3, ST11, ST22, ST32, ST19, ST16, and ST7.

Conclusion

These findings provided new insights into our understanding of the epidemiology and genetic characteristics of S. haemolyticus in dairy farms to inform interventions limiting the spread of AMR in dairy production.

Assessing the effects of limestone dust and lead pollution on the ecophysiology of some selected urban tree species

Soil and air pollution caused by heavy metals and limestone dust are prevalent in urban environments and they are an alarming threat to the environment and humans. This study was designed to investigate the changes in morphological and physiological traits of three urban tree species seedlings (Bombax ceiba, Conocarpus lancifolius, and Eucalyptus camaldulensis) under the individual as well as synergetic effects of heavy metal lead (Pb) and limestone dust toxicities. The tree species were grown under controlled environmental conditions with nine treatments consisting of three levels of dust (0, 10, and 20 g) and three levels of Pb contaminated water irrigation (0, 5, and 10 mg L^-1). The results depicted that the growth was maximum in T₁ and minimum in T₉ for all selected tree species. B. ceiba performed better under the same levels of Pb and limestone dust pollution as compared with the other two tree species. The B. ceiba tree species proved to be the most tolerant to Pb and limestone pollution by efficiently demolishing oxidative bursts by triggering SOD, POD, CAT, and proline contents under different levels of lead and dust pollution. The photosynthetic rate, stomatal conductance, evapotranspiration rate, and transpiration rate were negatively influenced in all three tree species in response to different levels of lead and dust applications. The photosynthetic rate was 1.7%, 3.1%, 7.0%, 11.03%, 16.2%, 23.8%, 24.8%, and 30.7%, and the stomatal conductance was 5%, 10.5%, 23.5%, 40%, 50.01%, 61.5%, 75%, and 90.9%, greater in T₂, T₃, T₄, T₅, T₆, T₇, T₈, and T₉ plants of B. ceiba, respectively, as compared to T₁. Based on the findings, among these three tree species, B. ceiba is strongly recommended for planting in heavy metal and limestone dust-polluted areas followed by E. camaldulensis and C. lancifolius due to their better performance and efficient dust and heavy metal-scavenging capability.

A near-complete genome assembly of Brassica rapa provides new insights into the evolution of centromeres

Brassica rapa comprises many important cultivated vegetables and oil crops. However, Chiifu v3.0, the current B. rapa reference genome, still contains hundreds of gaps. Here, we presented a near-complete genome assembly of B. rapa Chiifu v4.0, which was 424.59 Mb with only two gaps, using Oxford Nanopore Technology (ONT) ultralong-read sequencing and Hi-C technologies. The new assembly contains 12 contigs, with a contig N50 of 38.26 Mb. Eight of the ten chromosomes were entirely reconstructed in a single contig from telomere to telomere. We found that the centromeres were mainly invaded by ALE and CRM long terminal repeats (LTRs). Moreover, there is a high divergence of centromere length and sequence among B. rapa genomes. We further found that centromeres are enriched for Copia invaded at 0.14 MYA on average, while pericentromeres are enriched for Gypsy LTRs invaded at 0.51 MYA on average. These results indicated the different invasion mechanisms of LTRs between the two structures. In addition, a novel repetitive sequence PCR630 was identified in the pericentromeres of B. rapa. Overall, the near-complete genome assembly, B. rapa Chiifu v4.0, offers valuable tools for genomic and genetic studies of Brassica species and provides new insights into the evolution of centromeres.

Two salivary proteins Sm10 and SmC002 from grain aphid Sitobion miscanthi modulate wheat defense and enhance aphid performance

The grain aphid Sitobion miscanthi is a serious pest of wheat that causes severe economic damage by sucking phloem sap and transmitting plant viruses. Here, two putative salivary effector homologs from S. miscanthi (Sm10 and SmC002) were selected based on sequence similarity to other characterized aphid candidate effectors. These effectors were then delivered into wheat cells separately via the type III secretion system of Pseudomonas fluorescens to elucidate their functions in the regulation of plant defenses and host fitness. The results showed that the delivery of either Sm10 or SmC002 into wheat plants significantly suppressed callose deposition and affected the transcript levels of callose synthase genes. The expression levels of salicylic acid (SA)-associated defense genes were upregulated significantly in wheat leaves carrying either Sm10 or SmC002. Moreover, LC-MS/MS analysis revealed that wheat SA levels significantly increased after the delivery of the two effectors. The results of aphid bioassays conducted on the wheat plants carrying Sm10 or SmC002 showed significant increases in the survival and fecundity of S. miscanthi. This study demonstrated that the Sm10 and SmC002 salivary effectors of S. miscanthi enhanced host plant susceptibility and benefited S. miscanthi performance by regulating wheat defense signaling pathways.

A highly efficient genetic transformation system for broccoli and subcellular localization

INTRODUCTION

Agrobacterium-mediated genetic transformation has been widely used for the identification of functional genes and regulatory and developmental mechanisms in plants. However, there are still some problems of low genetic transformation efficiency and high genotype dependence in cruciferous crops.

METHODS

In this study, broccoli, a worldwide Brassica crop, was used to investigate the effects of genotype, explant type, concentration of hygromycin B used during seedling selection, overexpression vector type, RNAi and CRISPR/cas9 on the genetic transformation efficiency. At the same time, two vectors, PHG-031350 and PHG-CRa, were used for subcellular localization of the glucoraphanin synthesis-related gene FMOGS-OX5 and clubroot resistance gene by a PEG-Ca2+-mediated transient transformation system for broccoli protoplasts. Finally, the Agrobacterium-mediated genetic transformation system of broccoli was optimized and improved.

RESULTS AND DISCUSSION

This study showed that hypocotyl explants are more suitable for Agrobacterium-mediated transgene and CRISPR/Cas9 gene editing of broccoli. In contrast to previous studies, we found that 5 mg/L hygromycin B was more advantageous for the selection of resistant broccoli sprouts, and genotype 19B42 reached the highest transformation rate of 26.96%, which is higher than that in Brassica oleracea crops. In addition, the inbred line 19B42 successfully achieved high genetic transformation of overexpression, RNAi and CRISPR/Cas9 vectors; thus, it is powerful recipient material for the genetic transformation of broccoli. Subcellular localization proved that the glucoraphanin metabolism-related gene Bol031350 and clubroot resistance gene CRa were both expressed in the cytoplasm and nucleus, which provided a scientific basis for studying the regulation of glucosinolate metabolism and clubroot resistance in cruciferous crops. Therefore, these findings will provide new insight into the improvement of the genetic transformation and molecular breeding of Brassica oleracea crops.

Development of a MAGIC population and high-resolution quantitative trait mapping for nicotine content in tobacco

Multiparent Advanced Generation Inter-Cross (MAGIC) population is an ideal genetic and breeding material for quantitative trait locus (QTL) mapping and molecular breeding. In this study, a MAGIC population derived from eight tobacco parents was developed. Eight parents and 560 homozygous lines were genotyped by a 430K single-nucleotide polymorphism (SNP) chip assay and phenotyped for nicotine content under different conditions. Four QTLs associated with nicotine content were detected by genome-wide association mapping (GWAS), and one major QTL, named qNIC7-1, was mapped repeatedly under different conditions. Furthermore, by combining forward mapping, bioinformatics analysis and gene editing, we identified an ethylene response factor (ERF) transcription factor as a candidate gene underlying the major QTL qNIC7-1 for nicotine content in tobacco. A presence/absence variation (PAV) at qNIC7-1 confers changes in nicotine content. Overall, the large size of this MAGIC population, diverse genetic composition, balanced parental contributions and high levels of recombination all contribute to its value as a genetic and breeding resource. The application of the tobacco MAGIC population for QTL mapping and detecting rare allelic variation was demonstrated using nicotine content as a proof of principle.

Integrating GWAS and transcriptomics to identify candidate genes conferring heat tolerance in rice

INTRODUCTION

Rice (Oryza sativa L.) production is being challenged by global warming. Identifying new loci and favorable alleles associated with heat tolerance is crucial to developing rice heat-tolerant varieties.

METHODS

We evaluated the heat tolerance at the seedling stage using 620 diverse rice accessions. A total of six loci associated with heat tolerance were identified by a genome-wide association study (GWAS) with ~2.8 million single nucleotide polymorphisms (SNPs).

RESULTS

Among the six detected loci, qHT7 harbored the strongest association signal and the most associated SNPs. By comparing the transcriptomes of two representative accessions with contrasting heat tolerance, LOC_Os07g48710 (OsVQ30) was selected as a promising candidate gene in qHT7 due to the significant difference in its expression level between the two accessions. Haplotype 4 (Hap4) of LOC_Os07g48710 was determined as the favorable haplotype for heat tolerance via the gene-based haplotype analysis. The heat-tolerant haplotype LOC_Os07g48710Hap4 is highly enriched in the tropical Geng/Japonica accessions, and its frequency has decreased significantly during the improvement process of rice varieties.

DISCUSSION

Based on the GWAS and transcriptomics integrated results, a hypothetical model modulated by qHT7 in response to heat stress was proposed. Our results provide valuable candidate genes for improving rice heat tolerance through molecular breeding.

Genetic mapping and molecular characterization of the delayed green gene dg in watermelon (Citrullus lanatus)

Leaf color mutants are common in higher plants that can be used as markers in crop breeding and are important tools in understanding regulatory mechanisms of chlorophyll biosynthesis and chloroplast development. Genetic analysis was performed by evaluating F₁, F₂ and BC₁ populations derived from two parental lines (Charleston gray with green leaf color and Houlv with delayed green leaf color), suggesting that a single recessive gene controls the delayed green leaf color. In this study, the delayed green mutant showed a conditional pale green leaf color at the early leaf development but turned to green as the leaf development progressed. Delayed green leaf plants showed reduced pigment content, photosynthetic, chlorophyll fluorescence parameters, and impaired chloroplast development compared with green leaf plants. The delayed green (dg) locus was mapped to 7.48 Mb on chromosome 3 through bulk segregant analysis approach, and the gene controlling delayed green leaf color was narrowed to 53.54 kb between SNP130 and SNP135 markers containing three candidate genes. Sequence alignment of the three genes indicated that there was a single SNP mutation (G/A) in the coding region of ClCG03G010030 in the Houlv parent, which causes an amino acid change from Arginine to Lysine. The ClCG03G010030 gene encoded FtsH extracellular protease protein family is involved in early delayed green leaf development. The expression level of ClCG03G010030 was significantly reduced in delayed green leaf plants than in green leaf plants. These results indicated that the ClCG03G010030 might control watermelon green leaf color and the single SNP variation in ClCG03G010030 may result in early delayed green leaf color development during evolutionary process.

Electrochemical properties of roots determine antibiotic adsorption on roots

The adsorption behaviors and transfer pathways of antibiotics in plant-soil system are greatly influenced by the electrochemical properties of both soil particles and plant roots. However, the effects of roots electrochemical properties on antibiotic adsorption are largely unknown. Here, the fresh soybean, maize, and wheat roots with different electrochemical properties were obtained from hydroponic cultivation, and the adsorption processes and mechanisms of doxycycline, tetracycline, sulfadiazine, and norfloxacin on roots under various environmental conditions were investigated. Results showed that the adsorption amount of antibiotics on roots increased with the initial concentration of antibiotics. The coexisting low-molecular weight organic acids and anions inhibited the antibiotic adsorption on roots. The soybean roots performed strong adsorption ability compared with the maize and wheat roots driven by the variations in root electrochemical properties. This study demonstrates the significance of electrochemical interactions between antibiotics and roots in plant-soil system and can contribute to the more accurate risk assessment and effective pollution control of antibiotics.

Effects of chicken manure substitution for mineral nitrogen fertilizer on crop yield and soil fertility in a reduced nitrogen input regime of North-Central China

Organic manure has been proposed to substitute part of the chemical fertilizers. However, past research was usually conducted in regimes with excessive nitrogen (N) fertilization, which was not conducive to the current national goal of green and sustainable development. Therefore, exploring the potential of organic fertilizer substitution for mineral N fertilizer under regimes with reduced N inputs is important to further utilize organic fertilizer resources and establish sustainable nutrient management recommendations in the winter wheat (Triticum aestivum L.) - summer maize (Zea mays L.) rotation system in North-central China. In this study, a 4-year field experiment was conducted to investigate the effects of different chicken manure substitution ratios on crop yield, N recovery efficiency (REN), soil N and soil organic matter contents, to clarify the optimal organic substitution ratio of N fertilizer under reduced N application (from 540 kg N ha^-1 year^-1 to 400 kg N ha^-1 year^-1). Six substitution ratios were assessed: 0%, 20%, 40%, 60%, 80% and 100% under 200 kg N ha^-1 per crop season, respectively, plus a control with no N application from chemical fertilizer or chicken manure. Results showed that the highest yield was achieved under the 20% substitution ratio treatment, with 1.1% and 2.3% higher yield than chemical N alone in wheat season and maize seasons, respectively. At the chicken manure substitution ratios of 20% in wheat season and 20%-40% in maize season, the highest REN reached to 31.2% and 26.1%, respectively. Chicken manure application reduced soil residual inorganic N with increasing substitution ratio. All organic substitution treatments increased soil organic matter and total N content. Implementing 20% organic substitution in wheat season and 20%-40% in maize season under the reduced N application regime in the North-central China is therefore recommended in order to achieve high crop yields and REN, improve soil fertility and enhance livestock manure resource utilization.

A high-efficiency PEG-Ca2+-mediated transient transformation system for broccoli protoplasts

Transient transformation of plant protoplasts is an important method for studying gene function, subcellular localization and plant morphological development. In this study, an efficient transient transformation system was established by optimizing the plasmid concentration, PEG4000 mass concentration and genotype selection, key factors that affect transformation efficiency. Meanwhile, an efficient and universal broccoli protoplast isolation system was established. Using 0.5% (w/v) cellulase R-10 and 0.1% (w/v) pectolyase Y-23 to hydrolyze broccoli cotyledons of three different genotypes for 3 h, the yield was more than 5×10⁶/mL/g, and the viability was more than 95%, sufficient to meet the high standards for protoplasts to be used in various experiments. The average transformation efficiency of the two plasmid vectors PHG-eGFP and CP507-YFP in broccoli B1 protoplasts were 61.4% and 41.7%, respectively. Using this system, we successfully performed subcellular localization of the products of three target genes (the clubroot resistance gene CRa and two key genes regulated by glucosinolates, Bol029100 and Bol031350).The results showed that the products of all three genes were localized in the nucleus. The high-efficiency transient transformation system for broccoli protoplasts constructed in this study makes it possible to reliably acquire high-viability protoplasts in high yield. This research provides important technical support for international frontier research fields such as single-cell sequencing, spatial transcriptomics, plant somatic hybridization, gene function analysis and subcellular localization.

Widely targeted metabolomics analysis reveals the mechanism of quality improvement of flue-cured tobacco

Flue-curing of top leaves with stems is a widely applied curing technology. Owing to the presence of stems, the quality of flue-cured leaves was significantly improved. However, the contribution of stems to flue-cured leaves is still unknown. In this study, the differences in physicochemical properties and metabolomics data between separated leaves (stem(-)) and leaves with stems (stem(+)) were investigated. The metabolic profiling of stem(+) was significantly different from that of stem(-), with phytohormone indole-3-acetic acid (IAA) being one of the most differential metabolites. The presence of stems reduced the rate of water loss in leaves, which led to less ROS accumulation, higher antioxidant enzyme activities and a lower level of membrane lipid peroxidation in stem(+) than in stem(-). The presence of stems also helped maintain the cellular membrane integrity of leaf cells by preventing the accumulation of IAA in leaf cells. Better cellular membrane integrity during flue-curing means a lower risk of leaf browning. In addition, stem(+) had a lower starch content than stem(-) because of a higher level of amylase activity. In summary, these results indicated that the presence of stems caused metabolism changes in leaves, prevented flue-cured leaves from browning and enhanced starch degradation in leaves during flue-curing.

Hemocyte response to treatment of susceptible and resistant Asian corn borer (Ostrinia furnacalis) larvae with Cry1F toxin from Bacillus thuringiensis

Midgut receptors have been recognized as the major mechanism of resistance to Cry proteins in lepidopteran larvae, while there is a dearth of data on the role of hemocyte's response to Cry intoxication and resistance development. We aimed at investigating the role of circulating hemocytes in the intoxication of Cry1F toxin in larvae from susceptible (ACB-BtS) and resistant (ACB-FR) strains of the Asian corn borer (ACB), Ostrinia furnacalis. Transcriptome and proteome profiling identified genes and proteins involved in immune-related (tetraspanin and C-type lectins) and detoxification pathways as significantly up-regulated in the hemocytes of Cry1F treated ACB-FR. High-throughput in vitro assays revealed the binding affinity of Cry1F with the tetraspanin and C-type lectin family proteins. We found significant activation of MAPKinase (ERK 1/2, p38α, and JNK 1/2) in the hemocytes of Cry1F treated ACB-FR. In testing plausible crosstalk between a tetraspanin (CD63) and downstream MAPK signaling, we knocked down CD63 expression by RNAi and detected an alteration in JNK 1/2 level but a significant increase in susceptibility of ACB-FR larvae to Cry1F toxin. Information from this study advances a change in knowledge on the cellular immune response to Cry intoxication and its potential role in resistance in a lepidopteran pest.

Poly(thioctic acid): From Bottom-Up Self-Assembly to 3D-Fused Deposition Modeling Printing

Inspired by the bottom-up assembly in nature, an artificial self-assembly pattern is introduced into 3D-fused deposition modeling (FDM) printing to achieve additive manufacturing on the macroscopic scale. Thermally activated polymerization of thioctic acid (TA) enabled the bulk construction of poly(TA), and yielded unique time-dependent self-assembly. Freshly prepared poly(TA) can spontaneously and continuously transfer into higher-molecular-weight species and low-molecular-weight TA monomers. Poly(TA) and the newly formed TA further assembled into self-reinforcing materials via microscopic-phase separation. Bottom-up self-assembly patterns on different scales are fully realized by 3D FDM printing of poly(TA): thermally induced polymerization of TA (microscopic-scale assembly) to poly(TA) and 3D printing (macroscopic-scale assembly) of poly(TA) are simultaneously achieved in the 3D-printing process; after 3D printing, the poly(TA) modes show mechanically enhanced features over time, arising from the microscopic self-assembly of poly(TA) and TA. This study clearly demonstrates that micro- and macroscopic bottom-up self-assembly can be applied in 3D additive manufacturing.

Physiological and metabolic analyses provide insight into soybean seed resistance to fusarium fujikuroi causing seed decay

Seed-borne pathogens cause diverse diseases at the growth, pre- and post-harvest stage of soybean resulting in a large reduction in yield and quality. The physiological and metabolic aspects of seeds are closely related to their defense against pathogens. Recently, Fusarium fujikuroi has been identified as the dominant seed-borne fungi of soybean seed decay, but little information on the responses of soybean seeds induced by F. fujikuroi is available. In this study, a time-course symptom development of seed decay was observed after F. fujikuroi inoculation through spore suspension soaking. The germination rate and the contents of soluble sugar and soluble protein were significantly altered over time. Both chitinase and β-1,3-glucanase as important fungal cell wall-degrading enzymes of soybean seeds were also rapidly and transiently activated upon the early infection of F. fujikuroi. Metabolic profile analysis showed that the metabolites in glycine, serine, and threonine metabolism and tryptophan metabolism were clearly induced by F. fujikuroi, but different metabolites were mostly enriched in isoflavone biosynthesis, flavone biosynthesis, and galactose pathways. Interestingly, glycitein and glycitin were dramatically upregulated while daidzein, genistein, genistin, and daidzin were largely downregulated. These results indicate a combination of physiological responses, cell wall-related defense, and the complicated metabolites of soybean seeds contributes to soybean seed resistance against F. fujikuroi, which are useful for soybean resistance breeding.

Identification of QTL and candidate genes associated with biomass yield and Feed Quality in response to water deficit in alfalfa (Medicago sativa L.) using linkage mapping and RNA-Seq

Biomass yield and Feed Quality are the most important traits in alfalfa (Medicago sativa L.), which directly affect its economic value. Drought stress is one of the main limiting factors affecting alfalfa production worldwide. However, the genetic and especially the molecular mechanisms for drought tolerance in alfalfa are poorly understood. In this study, linkage mapping was performed in an F1 population by combining 12 phenotypic data (biomass yield, plant height, and 10 Feed Quality-related traits). A total of 48 significant QTLs were identified on the high-density genetic linkage maps that were constructed in our previous study. Among them, nine main QTLs, which explained more than 10% phenotypic variance, were detected for biomass yield (one), plant height (one), CP (two), ASH (one), P (two), K(one), and Mg (one). A total of 31 candidate genes were identified in the nine main QTL intervals based on the RNA-seq analysis under the drought condition. Blast-P was further performed to screen candidate genes controlling drought tolerance, and 22 functional protein candidates were finally identified. The results of the present study will be useful for improving drought tolerance of alfalfa varieties by marker-assisted selection (MAS), and provide promising candidates for further gene cloning and mechanism study.

Mitogen-activated protein kinase TaMPK3 suppresses ABA response by destabilising TaPYL4 receptor in wheat

Abscisic acid (ABA) receptors are considered as the targeted manipulation of ABA sensitivity and water productivity in plants. Regulation of their stability or activity will directly affect ABA signalling. Mitogen-activated protein kinase (MAPK) cascades link multiple environmental and plant developmental cues. However, the molecular mechanism of ABA signalling and MAPK cascade interaction remains largely elusive. TaMPK3 overexpression decreases drought tolerance and wheat sensitivity to ABA, significantly weakening ABA's inhibitory effects on growth. Under drought stress, overexpression lines show lower survival rates, shoot fresh weight and proline content, but higher malondialdehyde levels at seedling stage, as well as decreased grain width and 1000 grain weight in both glasshouse and field conditions at the adult stage. TaMPK3-RNAi increases drought tolerance. TaMPK3 interaction with TaPYL4 leads to decreased TaPYL4 levels by promoting its ubiquitin-mediated degradation, whereas ABA treatment diminishes TaMPK3-TaPYL interactions. In addition, the expression of ABA signalling proteins is impaired in TaMPK3-overexpressing wheat plants under ABA treatment. The MPK3-PYL interaction module was found to be conserved across monocots and dicots. Our results suggest that the MPK3-PYL module could serve as a negative regulatory mechanism for balancing appropriate drought stress response with normal plant growth signalling in wheat.

Effects of high-altitude hypoxic environment on colonic inflammation, intestinal barrier and gut microbiota in three-way crossbred commercial pigs

In recent years, the three-way crossbred commercial pigs are extensively cultured in Tibet. However, there have been few studies about the effect of high-altitude hypoxic environment on intestinal health of them. Therefore, we selected Tibetan pigs (TP) and the three-way crossbred commercial pigs (CP-H) living in the Tibet (3,500–3,700 m in altitude) as a positive control group and treatment group, respectively. The three-way crossbred commercial pigs (CP-L) living at altitudes 800–1,000 m sea level were selected as a negative control group. The colonic chyme, colonic mucosa, colonic tissue and serum samples were collected for the detection of gut microbiota and intestinal inflammation. The results showed that high-altitude hypoxic environment promoted the occurrence of colonic inflammation, disrupted the colonic barrier to some extent. And Hematoxylin–Eosin (HE) staining revealed that mild inflammatory cell infiltration was observed in colon of CP-H. 16S rRNA gene sequencing revealed that the microbial community composition of CP-H was changed compared with CP-L. Gut bacterial communities formed distinctly different clusters in principal coordinates analysis (PCoA) space, and Chao 1 index of CP-H was also decreased. At the genus level, Terrisporobacter showed greater enrichment in the CP-H than lower-altitude pigs. Colstridium-sensu-stricto-1 showed lower enrichment in the CP-H than lower-altitude pigs. However, the concentration of valeric acid in colonic chyme of CP-H was higher than CP-L and TP. Correlation analysis indicated that Terrisporobacter was positively associated with the relative mRNA expression level of IL-1β and the content of lipopolysaccharide (LPS), and was negatively correlated with the relative mRNA expression level of IL-10. The Streptococcus was positively associated with the concentrations of valerate. In summary, high-altitude hypoxic environment changed compositions of gut microbiota, promoted the occurrence of colonic inflammation, and disrupted intestinal barrier of the three-way crossbred commercial pigs.

Effects of rearing systems on the eggshell quality, bone parameters and expression of genes related to bone remodeling in aged laying hens

Public concerns regarding animal welfare are changing the selection of rearing systems in laying hens. This study investigated the effects of rearing systems on eggshell quality, bone parameters and relative expression levels of genes related to bone remodeling in aged laying hens. A total of 2,952 55-day-old Jing Tint Six pullets were randomly assigned to place in the conventional caging system (CCS) or aviary system (AVS) and kept until 95 weeks of age. The AVS group delayed the decrease of eggshell quality and alleviated the symptoms of osteoporosis in the humerus rather than in the femur. Eggshell breaking strength, thickness, weight, weight ratio, stiffness and fracture toughness were decreased linearly with age (from 55 to 95 weeks of age, p < 0.05). The AVS group had higher eggshell breaking strength, stiffness and fracture toughness than the CCS group (p < 0.05). Higher total calcium and phosphorus per egg were presented in the AVS group at 95 weeks of age (p < 0.05). At 95 weeks of age, the AVS group had a humerus with higher weight, volume, length, midpoint perimeter, cortical index, fat-free dry weight, ash content, total calcium per bone, total phosphorus per bone, average bone mineral density, strength, stiffness and work to fracture compared to the CCS group (p < 0.05). Such differences did not appear in the femur. The relative expression levels of alkaline phosphatase (ALP) and osteocalcin (OCN) genes in the femur and hormone receptors (vitamin D receptor (VDR), estrogen receptor alpha (ERα) and fibroblast growth factor 23 (FGF23)) genes in the humerus were significantly upregulated (p < 0.05) in the AVS group. The level of tartrate-resistant acid phosphatase (TRAP) transcripts was also increased (p < 0.05) in the femur of the AVS group. Overall, compared with the CCS, the AVS alleviated the deterioration of eggshell and bone qualities of aged laying hens, which may be related to the changes in the expression of genes associated with bone remodeling.

Escherichia coli O88 induces intestinal damage and inflammatory response through the oxidative phosphorylation and ribosome pathway in Pekin ducks

Colibacillosis is one of the major health threats in the poultry industry worldwide. Understanding the pathogenic mechanisms involved in Escherichia coli-induced inflammatory response may lead to the development of new therapies to combat the disease. To address this, a total of 96 1-day-old male lean Pekin ducklings were employed and randomly allocated to two treatments, each with six replicates of eight ducks. Ducks in the experiment group (EG) and the control group (CG) were separately orally administered with 0.2 ml of pathogenic E. coli O88 (3 × 109 CFU/ml) or equivalent volumes of 0.9% sterile saline solution on day 7, two times with an 8-h interval. Serum and intestinal samples were collected on days 9, 14, and 28. Results showed that ducks challenged with E. coli had lower average daily gain and higher feed intake/weight gain during days 9–14 and overall (P < 0.05). Histopathological examination showed that E. coli decreased the villus height and the ratio of villus height/crypt depth in the jejunum (P < 0.05) on days 9 and 14. The intestinal barrier was disrupted, presenting in E. coli ducks having higher serum DAO and D-LA on days 9 and 14 (P < 0.05) and greater content of serum LPS on day 9 (P < 0.05). Escherichia coli infection also triggered a systemic inflammatory response including the decrease of the serum IgA, IgM, and jejunal sIgA on day 14 (P < 0.05). In addition to these, 1,062 differentially expressed genes were detected in the jejunum tissues of ducks by RNA-seq, consisting of 491 upregulated and 571 downregulated genes. Based on the KEGG database, oxidative phosphorylation and the ribosome pathway were the most enriched. These findings reveal the candidate pathways and genes that may be involved in E. coli infection, allow a better understanding of the molecular mechanisms of inflammation progression and may facilitate the genetic improvement of ducks, and provide further insights to tackle the drug sensitivity and animal welfare issues.

Characterization of NAC transcription factor NtNAC028 as a regulator of leaf senescence and stress responses

NAC proteins constitute one of the largest transcription factor families and are involved in regulation of plant development and stress responses. Our previous transcriptome analyses of tobacco revealed a significant increase in the expression of NtNAC028 during leaf yellowing. In this study, we found that NtNAC028 was rapidly upregulated in response to high salinity, dehydration, and abscisic acid (ABA) stresses, suggesting a vital role of this gene in abiotic stress response. NtNAC028 loss-of-function tobacco plants generated via CRISPR-Cas9 showed delayed leaf senescence and increased tolerance to drought and salt stresses. Meanwhile NtNAC028 overexpression led to precocious leaf senescence and hypersensitivity to abiotic stresses in Arabidopsis, indicating that NtNAC028 functions as a positive regulator of natural leaf senescence and a negative regulator of stress tolerance. Furthermore, NtNAC028-overexpressing Arabidopsis plants showed lower antioxidant enzyme activities, higher reactive oxygen species (ROS), and H2O2 accumulation under high salinity, resulted in more severe oxidative damage after salt stress treatments. On the other hand, NtNAC028 mutation in tobacco resulted in upregulated expression of ROS-scavenging and abiotic stress-related genes, higher antioxidant enzyme activities, and enhanced tolerance against abiotic stresses, suggesting that NtNAC028 might act as a vital regulator for plant stress response likely by mediating ROS scavenging ability. Collectively, our results indicated that the NtNAC028 plays a key regulatory role in leaf senescence and response to multiple abiotic stresses.

Identification of the porcine IG-DMR and abnormal imprinting of DLK1-DIO3 in cloned pigs

Correct reprogramming of the DLK1-DIO3 imprinted region is critical for the development of cloned animals. However, in pigs, the imprinting and regulation of the DLK1-DIO3 region has not been systematically analyzed. The objective of this study was to investigate the imprinting status and methylation regulation of the DLK1-DIO3 region in wild-type and cloned neonatal pigs. We mapped the imprinting control region, IG-DMR, by homologous alignment and validated it in sperm, oocytes, fibroblasts, and parthenogenetic embryos. Subsequently, single nucleotide polymorphism-based sequencing and bisulfite sequencing polymerase chain reaction were conducted to analyze imprinting and methylation in different types of fibroblasts, as well as wild-type and cloned neonatal pigs. The results showed that Somatic cell nuclear transfer (SCNT) resulted in hypermethylation of the IG-DMR and aberrant gene expression in the DLK1-DIO3 region. Similar to wild-type pigs, imprinted expression and methylation were observed in the surviving cloned pigs, whereas in dead cloned pigs, the IG-DMR was hypermethylated and the expression of GTL2 was nearly undetectable. Our study reveals that abnormal imprinting of the DLK1-DIO3 region occurs in cloned pigs, which provides a theoretical basis for improving the cloning efficiency by gene editing to correct abnormal imprinting.

Biocontrol activity and action mechanism of Paenibacillus polymyxa strain Nl4 against pear Valsa canker caused by Valsa pyri

Pear Valsa canker caused by Valsa pyri is among the most destructive diseases of pear, which causes significant economic loss. The present study was developed to explore the biocontrol efficiency and underlying antagonistic mechanism of Paenibacillus polymyxa strain Nl4 against V. pyri. P. polymyxa strain Nl4, one of the 120 different endophytic bacterial strains from pear branches, exhibited strong inhibitory effects against the mycelial growth of V. pyri and caused hyphal malformation. Culture filtrate derived from strain Nl4 was able to effectively suppress mycelial growth of V. pyri, and was found to exhibit strong protease, cellulase and β-1, 3-glucanase activity. Through re-isolation assay, strain Nl4 was confirmed to be capable of colonizing and surviving in pear branch. Treatment with strain NI4 effectively protected against pear Valsa canker symptoms on detached pear twigs inoculated with V. pyri. Moreover, strain Nl4 promoted enhanced plant growth probably through the solubilization of phosphorus. Comparative transcriptomic analyses revealed that strain NI4 was able to suppress V. pyri growth in large part through the regulation of the expression of membrane- and energy metabolism-related genes in this pathogen. Further transcriptomic analyses of pear trees indicated that strain NI4 inoculation was associated with changes in the expression of genes associated with secondary metabolite biosynthesis, signal transduction, and cutin, suberine, and wax biosynthesis. Together, these data highlighted P. polymyxa strain Nl4 as a promising biocontrol agent against pear Valsa canker and investigated the possible mechanisms of strain Nl4 on control of this devastating disease.

A Comparison of Different Tissues Identifies the Main Precursors of Volatile Substances in Chicken Meat

Amino acids and fatty acids are the main precursors of volatile organic compounds (VOCs) in meat. The purpose of this study was to determine the main VOC components in chicken breast muscle (BM) and abdominal fat (AF) tissue, as well as the source of VOCs, to provide a basis for quality improvement of broilers. BM and AF served as experimental and control groups, and gas chromatography-mass spectrometry (GC-MS) and untargeted metabolomics were employed to identify the source of VOCs. The results revealed nine VOCs in BM and AF tissues, including hexanal, octanal, and nonanal. VOCs including 1-octen-3-ol, (E,E)-2, 4-nonadienal, and benzaldehyde were significantly elevated in BM compared with AF (p < 0.05), while heptane and diethyl disulphide showed the opposite trend (p < 0.05). Levels of hexanal, heptanal, and octanal were similar in the two tissues. Metabolites of VOCs in chicken BM were investigated by weighted co-expression network analysis. However, only blue module in BM tissue was positively correlated with hexanal (r = 0.66, p = 0.01), heptanal (r = 0.67, p = 0.008), and (E,E)-2,4-nonadienal (r = 0.88, p = 3E-05). L-tyrosine, L-asparagine, adenosine, and valine were the main precursors of (E,E)-2,4-nonadienal and heptanal in BM tissue. Amino acids are the main precursors of 1-octen-3-ol, (E,E)-2, 4-nonadienal, and heptanal in chicken meat, while fatty acids are the main precursors of diethyl disulfide. However, hexanal can be synthesized from amino acids and small amounts of fatty acids as precursors. These findings expand our understanding of VOCs in chicken.

The INFLORESCENCE DEFICIENT IN ABSCISSION-LIKE6 Peptide Functions as a Positive Modulator of Leaf Senescence in Arabidopsis thaliana

Leaf senescence is a highly coordinated process and has a significant impact on agriculture. Plant peptides are known to act as important cell-to-cell communication signals that are involved in multiple biological processes such as development and stress responses. However, very limited number of peptides has been reported to be associated with leaf senescence. Here, we report the characterization of the INFLORESCENCE DEFICIENT IN ABSCISSION-LIKE6 (IDL6) peptide as a regulator of leaf senescence. The expression of IDL6 was up-regulated in senescing leaves. Exogenous application of synthetic IDL6 peptides accelerated the process of leaf senescence. The idl6 mutant plants showed delayed natural leaf senescence as well as senescence included by darkness, indicating a regulatory role of IDL6 peptides in leaf senescence. The role of IDL6 as a positive regulator of leaf senescence was further supported by the results of overexpression analysis and complementation test. Transcriptome analysis revealed differential expression of phytohormone-responsive genes in idl6 mutant plants. Further analysis indicated that altered expression of IDL6 led to changes in leaf senescence phenotypes induced by ABA and ethylene treatments. The results from this study suggest that the IDL6 peptide positively regulates leaf senescence in Arabidopsis thaliana.

Multi-Trait Genomic Prediction Models Enhance the Predictive Ability of Grain Trace Elements in Rice

Multi-trait (MT) genomic prediction models enable breeders to save phenotyping resources and increase the prediction accuracy of unobserved target traits by exploiting available information from non-target or auxiliary traits. Our study evaluated different MT models using 250 rice accessions from Asian countries genotyped and phenotyped for grain content of zinc (Zn), iron (Fe), copper (Cu), manganese (Mn), and cadmium (Cd). The predictive performance of MT models compared to a traditional single trait (ST) model was assessed by 1) applying different cross-validation strategies (CV1, CV2, and CV3) inferring varied phenotyping patterns and budgets; 2) accounting for local epistatic effects along with the main additive effect in MT models; and 3) using a selective marker panel composed of trait-associated SNPs in MT models. MT models were not statistically significantly (p &lt; 0.05) superior to ST model under CV1, where no phenotypic information was available for the accessions in the test set. After including phenotypes from auxiliary traits in both training and test sets (MT-CV2) or simply in the test set (MT-CV3), MT models significantly (p &lt; 0.05) outperformed ST model for all the traits. The highest increases in the predictive ability of MT models relative to ST models were 11.1% (Mn), 11.5 (Cd), 33.3% (Fe), 95.2% (Cu) and 126% (Zn). Accounting for the local epistatic effects using a haplotype-based model further improved the predictive ability of MT models by 4.6% (Cu), 3.8% (Zn), and 3.5% (Cd) relative to MT models with only additive effects. The predictive ability of the haplotype-based model was not improved after optimizing the marker panel by only considering the markers associated with the traits. This study first assessed the local epistatic effects and marker optimization strategies in the MT genomic prediction framework and then illustrated the power of the MT model in predicting trace element traits in rice for the effective use of genetic resources to improve the nutritional quality of rice grain.

The Role of Incubation Conditions on the Regulation of Muscle Development and Meat Quality in Poultry

Muscle is the most abundant edible tissue in table poultry, which serves as an important source of high protein for humans. Poultry myofiber originates in the early embryogenic stage, and the overall muscle fiber number is almost determined before hatching. Muscle development in the embryonic stage is critical to the posthatch muscle growth and final meat yield and quality. Incubation conditions including temperature, humidity, oxygen density, ventilation and lighting may substantially affect the number, shape and structure of the muscle fiber, which may produce long-lasting effect on the postnatal muscle growth and meat quality. Suboptimal incubation conditions can induce the onset of myopathies. Early exposure to suitable hatching conditions may modify the muscle histomorphology posthatch and the final muscle mass of the birds by regulating embryonic hormone levels and benefit the muscle cell activity. The elucidation of the muscle development at the embryonic stage would facilitate the modulation of poultry muscle quantity and meat quality. This review starts from the physical and biochemical characteristics of poultry myofiber formation, and brings together recent advances of incubation conditions on satellite cell migration, fiber development and transformation, and subsequent muscle myopathies and other meat quality defects. The underlying molecular and cellular mechanisms for the induced muscle growth and meat quality traits are also discussed. The future studies on the effects of external incubation conditions on the regulation of muscle cell proliferation and meat quality are suggested. This review may broaden our knowledge on the regulation of incubation conditions on poultry muscle development, and provide more informative decisions for hatchery in the selection of hatching parameter for pursuit of more large muscle size and superior meat quality.

Effect of Ramie on the Production Performance of Laying Hens, and the Quality, Nutrient Composition, Antioxidation of the Eggs

Ramie (Boehmeria nivea), which is rich in protein, fatty acid, vitamins and minerals, has become a potential alternative feed resource for poultry, and has attracted more and more attentions in nutrition research. The objective of this study is to evaluate the effect of dietary ramie at different concentrations on the production performance of the hens, and the quality, nutrient composition, and antioxidation of the eggs. A total of 432 34-week-old Lohmann commercial laying hens were divided into four groups, that were fed with corn-soybean meal-based control diet, control mixed with ramie at concentrations of 3, 6, or 9% separately for 8 weeks. Results showed that dietary ramie did not affect production performance. And egg yolk color gradually deepened as the inclusion levels of ramie increased. Ramie at tested concentration could significantly reduce the content of malondialdehyde (MDA) (p = 0.002) and 3% ramie supplementation significantly increased total antioxidative capacity (T-AOC) concentrations in egg yolk compared to the control group (p = 0.033). In addition, dietary supplementation with 6% ramie significantly reduced total cholesterol (T-CHO) content (p < 0.05) compared with controls. For egg nutrient composition, compared with the control group, the addition of 6% ramie significantly increased (p < 0.05) total omega-3 polyunsaturated fatty acids (n-3PUFA) and phenylalanine (Phe) in yolk. In conclusion, dietary inclusion of 6% ramie was most effective in improving the color, antioxidative capability, and reducing T-CHO contents of the egg yolks without any negative impacts on the production performance of the hens.

Comprehensive Analysis Reveals the Genetic and Pathogenic Diversity of Ralstonia solanacearum Species Complex and Benefits Its Taxonomic Classification

Ralstonia solanacearum species complex (RSSC) is a diverse group of plant pathogens that attack a wide range of hosts and cause devastating losses worldwide. In this study, we conducted a comprehensive analysis of 131 RSSC strains to detect their genetic diversity, pathogenicity, and evolution dynamics. Average nucleotide identity analysis was performed to explore the genomic relatedness among these strains, and finally obtained an open pangenome with 32,961 gene families. To better understand the diverse evolution and pathogenicity, we also conducted a series of analyses of virulence factors (VFs) and horizontal gene transfer (HGT) in the pangenome and at the single genome level. The distribution of VFs and mobile genetic elements (MGEs) showed significant differences among different groups and strains, which were consistent with the new nomenclatures of the RSSC with three distinct species. Further functional analysis showed that most HGT events conferred from Burkholderiales and played a great role in shaping the genomic plasticity and genetic diversity of RSSC genomes. Our work provides insights into the genetic polymorphism, evolution dynamics, and pathogenetic variety of RSSC and provides strong supports for the new taxonomic classification, as well as abundant resources for studying host specificity and pathogen emergence.

Heterophil/Lymphocyte Ratio Level Modulates Salmonella Resistance, Cecal Microbiota Composition and Functional Capacity in Infected Chicken

The gastrointestinal microbiota plays a vital role in ensuring the maintenance of host health through interactions with the immune system. The Heterophil/Lymphocyte (H/L) ratio reflects poultry’s robustness and immune system status. Chickens with low H/L ratio are superior to the chickens with high H/L ratio in survival, immune response, and resistance to Salmonella infection, but the underlying mechanisms remain unclear. This study aimed to identify microorganisms associated with resistance to Salmonella Enteritidis infection in chickens based on the H/L ratio. The 16S rRNA and metagenomic analysis were conducted to examine microbiome and functional capacity between the 2 groups, and Short Chain Fatty Acids (SCFAs) and histopathology were conducted to explore the potential difference between susceptible and resistant groups at 7 and 21 days post-infection (dpi). The microbiome exploration revealed that low H/L ratio chickens, compared to high H/L ratio chickens, displayed a significantly higher abundance of Proteobacteria (Escherichia coli) and Bacteroidetes (Bacteroides plebeius) at 7 and 21 dpi, respectively. Anaerostipes (r = 0.63) and Lachnoclostridium (r = 0.63) were identified as bacterial genus significantly correlated with H/L (P < 0.001). Interestingly, Bacteroides was significantly and positively correlated with bodyweight post-infection (r = 0.72), propionate (r = 0.78) and valerate (r = 0.82) contents, while Salmonella was significantly and negatively correlated with bodyweight post-infection (r = − 0.67), propionate (r = − 0.61) and valerate (r = − 0.65) contents (P < 0.001). Furthermore, the comparative analysis of the functional capacity of cecal microbiota of the chickens with high and low H/L ratio revealed that the chickens with low H/L ratio possess more enriched immune pathways, lower antibiotic resistance genes and virulence factors compared to the chickens with high H/L ratio. These results suggest that the chickens with low H/L ratio are more resistant to Salmonella Enteritidis, and it is possible that the commensal Proteobacteria and Bacteroidetes are involved in this resistance against Salmonella infection. These findings provide valuable resources for selecting and breeding disease-resistant chickens.

Acute Endoplasmic Reticulum Stress Induces Inflammation Reaction, Complement System Activation, and Lipid Metabolism Disorder of Piglet Livers: A Proteomic Approach

Endoplasmic reticulum stress (ERS) is closely associated with the occurrence and development of many liver diseases. ERS models mostly include experimental animals such as rats and mice. However, pigs are more similar to humans with regards to digestion and metabolism, especially liver construction, yet few reports on ERS in pigs exist. In order to explore changes in the liver under ERS, we used tunicamycin (TM), which can cause liver jaundice and damage liver function, to establish acute ERS models in piglets using a low TM dosage (LD, 0.1 mg/kg body weight (bw)), high TM dosage (HD, 0.3 mg/kg bw), or vehicle for 48 h. We found that both LD- and HD-induced ERS, as verified by the ERS-linked proteins. Furthermore, the concentrations of the proinflammatory cytokines, namely, TNF-α and IL-6 were elevated in TM-treated piglet livers, and the plasma levels of IL-6 and CRP were also higher, indicating the occurrence of inflammation in TM-treated piglets. The complement system was activated in TM-treated piglets, as indicated by increased levels of complement factors and activation products C3, C5a, and AP50. In order to gain insights into the global changes in liver proteins under ERS, we performed an isobaric tag for relative and absolute quantitation (iTRAQ)-based proteomic analysis on the livers of HD- and vehicle-treated piglets. Proteomic analysis identified 311 differentially expressed proteins (DEPs) between the two groups, and a Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analysis suggested that the DEPs were mainly enriched in signaling pathways such as metabolic pathways, protein processing in the endoplasmic reticulum, and complement and coagulation cascades. Many proteins involved in protein folding, lipid transport, and oxidation were upregulated. Proteins involved in lipid synthesis were downregulated to alleviate liver steatosis, and most complement factors were upregulated to protect the body, and Pearson correlation analysis found that most of the DEPs in the complement and coagulation pathway were significantly correlated with plasma CRP, IL6 and AP50. Our results revealed that TM can activate ERS, marked by liver injury and steatosis, inflammatory reactions, and complement activation in piglets.

Transcriptome Analysis of Bovine Rumen Tissue in Three Developmental Stages

Rumen development is a crucial physiological challenge for ruminants. However, the molecular mechanism regulating rumen development has not been clearly elucidated. In this study, we investigated genes involved in rumen development in 13 rumen tissues from three developmental stages (birth, youth, and adult) using RNA sequencing. We identified that 6,048 genes were differentially expressed among three developmental stages. Using weighted correlation network analysis, we found that 12 modules were significantly associated with developmental stages. Functional annotation and protein–protein interaction (PPI) network analysis revealed that CCNB1, CCNB2, IGF1, IGF2, HMGCL, BDH1, ACAT1, HMGCS2, and CREBBP involved in rumen development. Integrated transcriptome with GWAS information of carcass weight (CW), stomach weight (SW), marbling score (MS), backfat thickness (BFT), ribeye area (REA), and lean meat weight (LMW), we found that upregulated DEGs (fold change 0∼1) in birth–youth comparison were significantly enriched with GWAS signals of MS, downregulated DEGs (fold change >3) were significantly enriched with GWAS signals of SW, and fold change 0∼1 up/downregulated DEGs in birth–adult comparison were significantly enriched with GWAS signals of CW, LMW, REA, and BFT. Furthermore, we found that GWAS signals for CW, LMW, and REA were enriched in turquoise module, and GWAS signals for CW was enriched in lightgreen module. Our study provides novel insights into the molecular mechanism underlying rumen development in cattle and highlights an integrative analysis for illustrating the genetic architecture of beef complex traits.

Influence of Dairy Cows Bedding Material on the Microbial Structure and Antibiotic Resistance Genes of Milk

The presence of pathogenic bacteria and antibiotic resistance genes (ARGs) in milk are among the most important issues related to the safety of dairy products and the health of consumers. However, despite that dairy cow are housed for long periods of time on different beddings, the effect of different bedding materials on the microbiota and presence of ARGs is unclear. In this study, the composition of microorganisms, and the presence of mastitis pathogens and 33 ARGs targeting seven antibiotics in raw milk produced from farms using sand bedding, rice husk bedding, and recycled manure solids (RMS) bedding were compared by amplicon sequencing and real-time quantitative PCR. The results showed that the microbial composition of milk was related to the microbiota of bedding. None of the mastitis pathogens were detected in milk from cows housed on sand bedding (S-M). The proportion of ARGs was highest in the S-M group and lowest in the milk from cows housed on RMS bedding (RMS-M) group. In general, the content of ARGs in RMS-M was the lowest, however, the RMS bedding may pose a threat to the breast health of dairy cows.

Genetic Drift and Purifying Selection Shaped Mitochondrial Genome Variation in the High Royal Jelly-Producing Honeybee Strain (Apis mellifera ligustica)

Mitochondrial genomes (mitogenomes) are involved in cellular energy metabolism and have been shown to undergo adaptive evolution in organisms with increased energy-consuming activities. The genetically selected high royal jelly-producing bees (RJBs, Apis mellifera ligustica) in China can produce 10 times more royal jelly, a highly nutritional and functional food, relative to unselected Italian bees (ITBs). To test for potential adaptive evolution of RJB mitochondrial genes, we sequenced mitogenomes from 100 RJBs and 30 ITBs. Haplotype network and phylogenetic analysis indicate that RJBs and ITBs are not reciprocally monophyletic but mainly divided into the RJB- and ITB-dominant sublineages. The RJB-dominant sublineage proportion is 6-fold higher in RJBs (84/100) than in ITBs (4/30), which is mainly attributable to genetic drift rather than positive selection. The RJB-dominant sublineage exhibits a low genetic diversity due to purifying selection. Moreover, mitogenome abundance is not significantly different between RJBs and ITBs, thereby rejecting the association between mitogenome copy number and royal jelly-producing performance. Our findings demonstrate low genetic diversity levels of RJB mitogenomes and reveal genetic drift and purifying selection as potential forces driving RJB mitogenome evolution.

Seleno-Amino Acids in Vegetables: A Review of Their Forms and Metabolism

Seleno-amino acids are safe, health-promoting compounds for humans. Numerous studies have focused on the forms and metabolism of seleno-amino acids in vegetables. Based on research progress on seleno-amino acids, we provide insights into the production of selenium-enriched vegetables with high seleno-amino acids contents. To ensure safe and effective intake of selenium, several issues need to be addressed, including (1) how to improve the accumulation of seleno-amino acids and (2) how to control the total selenium and seleno-amino acids contents in vegetables. The combined use of plant factories with artificial lighting and multiple analytical technologies may help to resolve these issues. Moreover, we propose a Precise Control of Selenium Content production system, which has the potential to produce vegetables with specified amounts of selenium and high proportions of seleno-amino acids.

Abscisic acid alleviates chilling injury in cold-stored peach fruit by regulating ethylene and hydrogen peroxide metabolism

Peach (Prunus persica (L.) Batsch) is susceptible to chilling injury under improper low-temperature storage (2°C-5°C). Previous research has shown that abscisic acid (ABA) alleviates chilling injury in fruits and vegetables, but the potential mechanism is still unclear. To explore its effectiveness and potential mechanism in alleviating chilling injury during cold storage, exogenous ABA was applied to peach fruit by immersion in 100 μmol L^-1 solutions for 10 min. In our experiment, ABA alleviated chilling injury by reducing hydrogen peroxide (H₂O₂) content and ethylene production. In addition, ABA inhibited the expression of the ethylene synthesis-related genes PpACO1 and PpEIN2. At the same time, ABA activated the antioxidant enzymatic pathway and the ascorbate-glutathione (AsA-GSH) cycle, the transcript abundance encoding genes related to antioxidant enzyme activities also changed correspondingly. The results suggested that ABA alleviated chilling injury by scavenging excessive H₂O₂ by promoting antioxidant enzymes and the AsA-GSH pathway.

Overexpression of NtCBL5A Leads to Necrotic Lesions by Enhancing Na+ Sensitivity of Tobacco Leaves Under Salt Stress

Many tobacco (Nicotiana tabacum) cultivars are salt-tolerant and thus are potential model plants to study the mechanisms of salt stress tolerance. The CALCINEURIN B-LIKE PROTEIN (CBL) is a vital family of plant calcium sensor proteins that can transmit Ca²⁺ signals triggered by environmental stimuli including salt stress. Therefore, assessing the potential of NtCBL for genetic improvement of salt stress is valuable. In our studies on NtCBL members, constitutive overexpression of NtCBL5A was found to cause salt supersensitivity with necrotic lesions on leaves. NtCBL5A-overexpressing (OE) leaves tended to curl and accumulated high levels of reactive oxygen species (ROS) under salt stress. The supersensitivity of NtCBL5A-OE leaves was specifically induced by Na⁺, but not by Cl^-, osmotic stress, or drought stress. Ion content measurements indicated that NtCBL5A-OE leaves showed sensitivity to the Na⁺ accumulation levels that wild-type leaves could tolerate. Furthermore, transcriptome profiling showed that many immune response-related genes are significantly upregulated and photosynthetic machinery-related genes are significantly downregulated in salt-stressed NtCBL5A-OE leaves. In addition, the expression of several cation homeostasis-related genes was also affected in salt-stressed NtCBL5A-OE leaves. In conclusion, the constitutive overexpression of NtCBL5A interferes with the normal salt stress response of tobacco plants and leads to Na⁺-dependent leaf necrosis by enhancing the sensitivity of transgenic leaves to Na⁺. This Na⁺ sensitivity of NtCBL5A-OE leaves might result from the abnormal Na⁺ compartmentalization, plant photosynthesis, and plant immune response triggered by the constitutive overexpression of NtCBL5A. Identifying genes and pathways involved in this unusual salt stress response can provide new insights into the salt stress response of tobacco plants.

Insight Into Pituitary lncRNA and mRNA at Two Estrous Stages in Small Tail Han Sheep With Different FecB Genotypes

The pituitary is a remarkably dynamic organ with roles in hormone (FSH and LH) synthesis and secretion. In animals with the FecB (fecundity Booroola) mutation, the pituitary experiences hormone fluctuations during the follicular-luteal transition, which is implicated in the expression and regulation of many genes and regulators. Long non-coding RNAs (lncRNAs) are a novel type of regulatory factors for the reproductive process. Nevertheless, the expression patterns of lncRNAs and their roles in FecB-mediated follicular development and ovulation remain obscure. Thus, we profiled the pituitary transcriptome during the follicular (F, 45 h after evacuation vaginal sponges) and luteal (L, 216 h after evacuation vaginal sponges) phases in FecB-mutant homozygous (BB) and wild-type (WW) Small Tail Han sheep. We identified 78 differentially expressed genes (DEGs) and 41 differentially expressed lncRNAs (DELs) between BB_F and BB_L, 32 DEGs and 26 DELs between BB_F and WW_F, 16 DEGs and 29 DELs between BB_L and WW_L, and 50 DEGs and 18 DELs between WW_F and WW_L. The results of real-time quantitative PCR (RT-qPCR) correlated well with the transcriptome data. In both the follicular and luteal phases, DEGs (GRID2, glutamate ionotropic receptor delta type subunit 2; ST14, ST14 transmembrane serine protease matriptase) were enriched in hormone synthesis, secretion, and action. MSTRG.47470 and MSTRG.101530 were the trans-regulated elements of ID1 (inhibitor of DNA binding 3, HLH protein) and the DEG ID3 (inhibitor of DNA binding 3, HLH protein), and EEF2 (eukaryotic translation elongation factor 2), respectively; these factors might be involved in melatonin and peptide hormone secretion. In the FecB-mediated follicular phase, MSTRG.125392 targeted seizure-related 6 homolog like (SEZ6L), and MSTRG.125394 and MSTRG.83276 targeted the DEG KCNQ3 (potassium voltage-gated channel subfamily Q member 3) in cis, while MSTRG.55861 targeted FKBP4 (FKBP prolyl isomerase 4) in trans. In the FecB-mediated luteal phase, LOC105613905, MSTRG.81536, and MSTRG.150434 modulated TGFB1, SMAD3, OXT, respectively, in trans. We postulated that the FecB mutation in pituitary tissue elevated the expression of certain genes associated with pituitary development and hormone secretion. Furthermore, this study provides new insights into how the pituitary regulates follicular development and ovulation, illustrated by the effect of the FecB mutation.