Soil temperature regime (STR) is important for soil classification and land use.  Generally, STR is delineated by estimating the mean annual soil temperature at a depth of 50 cm (MAST50) according to the Chinese Soil Taxonomy (CST).  However, delineating the STR of China remains a challenge due to the difficulties in accurately estimating MAST50.  The objectives of this study were to explore environmental factors that influence the spatial variation of MAST50 and generate an STR map for China.  Soil temperature measurements at 40 and 80 cm depth were collected from 386 National Meteorological Stations in China during 1971–2000.  The MAST50 was calculated as the average mean annual soil temperature (MAST) from 1971–2000 between 40 and 80 cm depths.  In addition, 2 048 mean annual air temperature (MAAT) measurements from 1971 to 2000 were collected from the National Meteorological Stations across China.  A zonal pedotransfer function (PTF) was developed based on the ensemble linear regression kriging model to predict the MAST50 in three topographic steps of China.  The results showed that MAAT was the most important variable related to the variation of MAST50.  The zonal PTF was evaluated with a 10% validation dataset with a mean absolute error (MAE) of 0.66°C and root mean square error (RMSE) of 0.78°C, which were smaller than the unified model with MAE of 0.83°C and RMSE of 0.96°C, respectively.  This study demonstrated that the zonal PTF helped improve the accuracy of the predicted MAST50 map.  Based on the prediction results, an STR map across China was generated to provide a consistent scientific base for the improvement and application of CST and land use support.

Enhancing host immunity is an effective way to reduce morbidity in chickens.  Heterophil to lymphocyte ratio (H/L) is associated with host disease resistance in birds.  Chickens with different H/L levels show different disease resistances.  However, the utility of the H/L as an indicator of immune function needs to be further analyzed.  In this study, a H/L directional breeding chicken line (Jingxing yellow chicken) was constructed, which has been bred for 12 generations.  We compared the function of heterophils, and combined statistical analysis to explore the candidate genes and pathways related to H/L.  The oxidative burst function of the heterophils isolated from the H/L selection line (G12) was increased (P=0.044) compared to the non-selection line (NS).  The 22.44 Mb genomic regions which annotated 300 protein-coding genes were selected in the genome of G9 (n=92) compared to NS (n=92) based on a genome-wide selective sweep.  Several selective regions were identified containing genes like interferon induced with helicase C domain 1 (IFIH1) and moesin (MSN) associated with the intracellular receptor signaling pathway, C–C motif chemokine receptor 6 (CCR6), dipeptidyl peptidase 4 (DPP4) and hemolytic complement (HC) associated with the negative regulation of leukocyte chemotaxis and tight junction protein 1 (TJP1) associated with actin cytoskeleton organization.  In addition, 45 genome-wide significant indels containing 29 protein-coding genes were also identified as associated with the H/L based on genome-wide association study (GWAS).  The expression of protein tyrosine phosphatase non-receptor type 5 (PTPN5) (r=0.75, P=0.033) and oxysterol binding protein like 5 (OSBPL5) (r=0.89, P=0.0027) were positively correlated with H/L.  Compared to the high H/L group, the expressions of PTPN5 and OSBPL5 were decreased (P<0.05) in the low H/L group of Beijing you chicken.  The A/A allelic frequency of indel 5_13108985 (P=3.85E–06) within OSBPL5 gradually increased from the NS to G5 and G9, and the individuals with A/A exhibited lower H/L than individuals with heterozygote A/ATCT (P=4.28E–04) and homozygous ATCT/ATCT (P=3.40E–05).  Above results indicated oxidative burst function of heterophils were enhanced, and 22.44 Mb genomic regions were selected with the directional selection of H/L.  In addition, PTPN5 and OSBPL5 genes were identified as H/L-related candidate genes.  These findings revealed the complex genetic mechanism of H/L related to immunity and will allow selection for improving chicken immunity based on the H/L

Carotenoids are an important component of the human diet, and fruit is a primary source of carotenoids.  The synthesis and regulation of carotenoids in fruit are important contributors to the formation of fruit quality.  In China, strawberry is one of the main seasonal fruits grown in the winter.  Previous studies have shown that light has a significant effect on the metabolism of anthocyanins, sugars, and polyphenols in strawberry.  However, the understanding of the role of light in regulating the metabolism of carotenoids in strawberry remains limited.  This study investigated the effects of blue, red, yellow-green, and white light on carotenoid metabolism in strawberry.  Blue light treatment promoted the synthesis of multiple carotenoids, including lutein, compared with the other three treatment groups.  The RNA sequencing data revealed that blue light treatment promoted the expression of lycopene ε-cyclase (LCYE), and the transient overexpression of LCYE in strawberry fruit promoted lutein accumulation in strawberry.  Overall, the results suggest that blue light can promote the synthesis of lutein in strawberry by inducing the expression of LCYE.

With the implementation of the C-strain vaccine, classical swine fever (CSF) has been under control in China, which is currently in a chronic atypical epidemic situation.  African swine fever (ASF) emerged in China in 2018 and spread quickly across the country. It is presently occurring sporadically due to the lack of commercial vaccines and farmers’ increased awareness of biosafety.  Atypical porcine pestivirus (APPV) was first detected in Guangdong Province, China, in 2016, which mainly harms piglets and has a local epidemic situation in southern China.  These three diseases have similar clinical symptoms in pig herds, which cause considerable losses to the pig industry.  They are difficult to be distinguished only by clinical diagnosis.  Therefore, developing an early and accurate simultaneous detection and differential diagnosis of the diseases induced by these viruses is essential.  In this study, three pairs of specific primers and Taq-man probes were designed from highly conserved genomic regions of CSFV (5´ UTR), African swine fever virus (ASFV) (B646L), and APPV (5´ UTR), followed by the optimization of reaction conditions to establish a multiplex real-time PCR detection assay.  The results showed that the method did not cross-react with other swine pathogens (porcine circovirus type 2 (PCV2), porcine reproductive and respiratory syndrome virus (PRRSV), foot-and-mouth disease virus (FMDV), pseudorabies virus (PRV), porcine parvovirus (PPV), and bovine viral diarrhea virus BVDV).  The sensitivity results showed that CSFV, ASFV, and APPV could be detected as low as 1 copy mL^–1; the repeatability results showed that the intra-assay and inter-assay coefficient of variation of ASFV, CSFV, and APPV was less than 1%.  Twenty-two virus samples were detected by the multiplex real-time PCR, compared with national standard diagnostic and patented method assay for CSF (GB/T 27540–2011), ASF (GB/T 18648–2020), and APPV (CN108611442A), respectively.  The sensitivity of this triple real-time PCR for CSFV, ASFV, and APPV was almost the same, and the  compliance results were the same (100%).  A total of 451 clinical samples were detected, and the results showed that the positive rates of CSFV, ASFV, and APPV were 0.22% (1/451), 1.3% (6/451), and 0% (0/451), respectively.  This assay provides a valuale tool for rapid detection and accurate diagnosis of CSFV, ASFV, and APPV.

Leaf-mining flies (Diptera: Agromyzidae) are a diverse family of small-bodied insects that feed on living plant tissues as larvae.  Various species in this family are considered globally invasive and have caused great agricultural economic losses.  In China, economically important vegetable crops have been seriously damaged by these pest insects, especially by species of the genus Liriomyza.  However, these species are difficult to differentiate because of their morphological similarities, and the Chinese fauna remains poorly known.  To explore the relevant pest species in China and their phylogeny, agromyzid leafminers were collected from 2016 to 2019, and identified based on morphological characteristics and DNA barcodes.  In total, 27 species from five genera of Agromyzidae were sampled and identified, including 16 species of Liriomyza.  Both mitochondrial and nuclear genes were used to reconstruct their phylogenetic relationships and estimate the divergence time.  Highly congruent and well-supported phylogenetic trees were obtained using the Bayesian inference and maximum-likelihood methods.  This analysis revealed two main clades in Liriomyza, and clade 2 was inferred to have diverged from clade 1 approximately 27.40 million years ago (95% highest posterior density: 23.03–31.52 million years ago) in the Oligocene.  Differences were observed in the distribution patterns and host associations between the Liriomyza clades.  Clade 2 species are distributed in cool, high-latitude environments, suggesting that they may have evolved into a cool-adapted lineage.

Investigating the dynamics and distribution of soil phosphorus (P) fractions can provide a basis for enhancing P utilization by crops.  Four treatments from a 29-year long-term experiment in black soil with maize cropping were involved in this study: no fertilizer (CK), inorganic nitrogen and potassium (NK), inorganic nitrogen, phosphorus, and potassium (NPK), and NPK plus manure (NPKM).  We analyzed soil P fractions in different soil layers using a modified Hedley sequential method.  The long-term NPKM treatment significantly increased total P by 0.6–1.6 times in the different soil layers.  The Olsen-P concentration far exceeded the environmental threshold for soil Olsen-P (50.6 mg kg^–1) in the NPKM treatment in the 0–60 cm soil profile.  Moreover, the concentrations and proportion of labile and partially labile inorganic P (Pi) fractions (i.e., NaHCO₃-extracted Pi, NaOH-extracted Pi, and dilute HCl-extracted Pi) to the sum of all P fractions (Pt) in the 0–60 cm soil profile were higher in the NPKM treatment than in the NPK treatment, indicating that manure could promote the transformation of non-labile into more labile forms of P in soil, possibly by manure reducing P fixation by soil particles.  Soil organic matter, Mehlich-3 extractable iron (Fe), and organic-bound aluminum were increased by fertilization, and were the main factors influencing the differences in the P fractions in the 0–20 cm soil layer.  Soil mineral components, i.e., free Fe oxide and CaCO₃, were the main factors influencing the P fractions in the subsoil.  The soil P transformation process varied with soil layer and fertilization.  Application of manure fertilizer can increase the labile (Olsen) P concentrations of the various soil layers, and thus should reduce the mineral P fertilizer requirement for crop growth and reduce potential environmental damage

High-moisture extrusion technology should be considered one of the best choices for producing plant-based meat substitutes with the rich fibrous structure offered by real animal meat products.  Unfortunately, the extrusion process has been seen as a “black box” with limited information about what occurs inside, causing serious obstacles in developing meat substitutes.  This study designed a high-moisture extrusion process and developed 10 new plant-based meat substitutes comparable to the fibrous structure of real animal meat.  The study used the Feature-Augmented Principal Component Analysis (FA-PCA) method to visualize and understand the whole extrusion process in three ways systematically and accurately.  It established six sets of mathematical models of the high-moisture extrusion process based on 8 000 pieces of data, including five types of parameters.  The FA-PCA method improved the R² values significantly compared with the PCA method.  The Way 3 was the best to predict product quality (Z), demonstrating that the gradually molecular conformational changes (Yⁿ´) were critical in controlling the final quality of the plant-based meat substitutes.  Moreover, the first visualization platform software for the high-moisture extrusion process has been established to clearly show the “black box” by combining the virtual simulation technology.  Through the software, some practice work such as equipment installation, parameter adjustment, equipment disassembly, and data prediction can be easily achieved.

Salmonella is one of the most common food-borne pathogens and its resistance in chicken can be improved through genetic selection.  The heterophils/lymphocytes (H/L) ratio in the blood reflects the immune system status of chicken.  We compared the genome data and spleen transcriptomes between the H/L ratio-selected and non-selected chickens, after Salmonella infection, aiming to identify the key genes participating in the antibacterial activity in the spleen.  The results revealed that, the selected population had stronger (P<0.05) liver resistance to Salmonella typhimurium (ST) than the non-selected population.  In the selected and non-selected lines, the identified differentiation genes encode proteins involved in biological processes or metabolic pathways that included the TGF-beta signaling pathway, FoxO signaling pathway, and Salmonella infection pathway.  The results of the analysis of all identified differentially expressed genes (DEGs) of spleen revealed that the G protein-coupled receptor (GPCR) and insulin-like growth factor (IGF-I) signaling pathways were involved in the Salmonella infection pathway.  Integrated analysis of DEGs and F_ST (fixation index), identified candidate genes involved in Salmonella infection pathway, such as GPR39, NTRK2, and ANXA1.  The extensive genomic changes highlight the polygenic genetic of the immune response in these chicken populations.  Numerous genes related to the immune performance are differentially expressed in the selected and non-selected lines and the selected lines has a higher resistance to Salmonella. 

The pre-mRNA processing factor Prp6 is an essential component of the U4/U6.U5 tri-small nuclear ribonucleoprotein (snRNP).  In a previous study, mutations were identified in the PRP6 ortholog in four suppressors of Fgprp4 that was deleted of the only kinase FgPrp4 among the spliceosome components in the plant pathogenic fungus Fusarium graminearum.  In this study, we identified additional suppressor mutations in FgPrp6 and determined the suppressive effects of selected mutations.  In total, 12 mutations of FgPRP6 were identified in 20 suppressors of Fgprp4 by sequencing analysis.  Whereas three mutation sites are in the linker region of FgPrp6, seven are in the first two HAT repeats.  RNA-seq analysis showed that suppressor mutations on different sites caused different splicing efficiency recovery.  The suppressive effects of E308K and R230H were verified.  Similar to human and fission yeast, the FgPrp6 was phosphorylated by the FgPrp4 kinase.  Interestingly, the conserved Prp4-phosphorylation sites T261, T219&T221, and predicted phosphorylation sites T199&T200 on FgPrp6 were dispensable for the function of FgPrp6 in hyphal growth and sexual reproduction but important in plant infection.  They are required for the infectious growth of F. graminearum in wheat lemma.  RNA-seq analysis of the wheat lemma infected with Fgprp6/FgPRP6^Δ199–221-GFP or Fgprp6/FgPRP6^Δ250–262-GFP showed that 28 and 35% introns had splicing defects, respectively, which may be responsible for their defects in plant infection.    

High-oleic acid peanut oil (HOPO) and extra-virgin olive oil (EVOO) have been reported previously to have an attenuating effect on metabolic syndrome (MS).  This study aimed to evaluate the metabolic effect of HOPO and EVOO supplementation in attenuating MS and the role of gut microbiota in regulating the metabolic profile.  Sprague-Dawley rats were continuously fed with a normal diet, high-fructose and high-fat (HFHF) diet, HFHF diet containing HOPO, or a HFHF diet containing EVOO for 12 weeks.  The metabolomics profiles of feces and serum samples were compared using untargeted metabolomics based on UPLC-Q/TOF-MS.  Partial Least Squares Discriminant Analysis (PLS-DA) was used to identify the potential fecal and serum biomarkers from different groups.  Correlation between gut microbiota and biomarkers was assessed, and pathway analysis of serum biomarkers was conducted.  Differences in metabolic patterns in feces and serum were observed among different groups.  There were 8 and 12 potential biomarkers in feces and 15 and 6 potential biomarkers in serum of HOPO group and EVOO group, respectively, suggesting that HOPO and EVOO supplementation mainly altered amino acids, peptides, and their analogs in feces and serum.  The branched-chain amino acids (BCAAs) biosynthesis pathway was identified as a major pathway regulated by HOPO or EVOO.  This study suggests that HOPO and EVOO supplementation ameliorate diet-induced MS, mainly via modulation of the BCAAs biosynthesis pathway.

Skeletal muscle development is closely related with the amount of meat production and its quality in chickens.  Natriuretic peptides (NPs) play an important role in myotube formation and fat oxidation of skeletal muscle in animals.  The effect of C-type natriuretic peptide (CNP), an important member of the NPs, and its underlying molecular mechanisms in skeletal muscle are incompletely understood.  Treatment of myoblasts with CNP led to enhanced proliferation/differentiation and significantly upregulated (P<0.05) mRNA expression of the CNP receptors natriuretic peptide receptor B (NPRB) and the clearance receptor C (NPRC).  In cells exposed to CNP, 142 differentially expressed genes (84 up-regulation and 58 down-regulation) (P<0.05) were identified by RNA-sequencing compared with those in control cells.  Sixteen genes were significantly enriched (P<0.05) in the metabolic pathway, and six of them (phospholipase C β4, phospholipase C β2, phosphoglycerate mutase 1, creatine kinase B, peroxiredoxin 6 and CD38) were closely related to skeletal muscle development and differentially expressed.  In conclusion, CNP stimulated differentiation of myoblasts by upregulating expression of the NPRB and NPRC receptors and enriching key genes in the metabolic pathway.  

Understanding the characteristics and influences of various factors on phosphorus (P) fractions is of significance for promoting the efficiency of soil P.  Based on long-term experiments on black soil, fluvo-aquic soil, and loess soil, which belong to Phaeozems, Cambisols, and Anthrosols in the World Reference Base for Soil Resources (WRB), respectively, five fertilization practices were selected and divided into three groups: no P fertilizer (CK/NK), balanced fertilizer (NPK/NPKS), and manure plus mineral fertilizer (NPKM).  Soil inorganic P (Pi) fractions and soil properties were analyzed to investigate the characteristics of the Pi fractions and the relationships between Pi fractions and various soil properties.  The results showed that the proportion of Ca₁₀-P in the sum of total Pi fractions was the highest in the three soils, accounting for 33.5% in black soil, 48.8% in fluvo-aquic soil, and 44.8% in loess soil.  Long-term fertilization practices resulted in periodic changes in soil Pi accumulation or depletion.  For black soil and fluvo-aquic soil, the Pi accumulation was higher in the late period (10–20 years) of fertilization than in the early period (0–10 years) under NPK/NPKS and NPKM, whereas the opposite result was found in loess soil.  The Pi accumulation occurred in all Pi fractions in black soil; mainly in Ca₈-P, Fe-P, and Ca₁₀-P in fluvo-aquic soil; and in Ca₂-P, Ca₈-P, and O-P in loess soil.  Under CK/NK, the soil Pi was depleted mainly in the early period in each of the three soils.  In addition to the labile Pi (Ca₂-P) and moderately labile Pi (Ca₈-P, Fe-P, Al-P), the Ca₁₀-P in black soil and fluvo-aquic soil and O-P in loess soil could also be used by crops.  Redundancy analysis showed that soil properties explained more than 90% of the variation in the Pi fractions in each soil, and the explanatory percentages of soil organic matter (SOM) were 43.6% in black soil, 74.6% in fluvo-aquic, and 38.2% in loess soil.  Consequently, decisions regarding the application of P fertilizer should consider the accumulation rate and the variations in Pi fractions driven by soil properties in non-acidic soils.

Cell wall architecture plays a key role in stalk strength and forage digestibility.  Lignin, cellulose, and hemicellulose are the three main components of plant cell walls, and they can impact stalk quality by affecting the structure and strength of the cell wall.  To explore cell wall development during secondary cell wall lignification in maize stalks, conventional and conditional genetic mapping were used to identify the dynamic quantitative trait loci (QTLs) of the cell wall components and digestibility traits during five growth stages after silking.  Acid detergent lignin (ADL), cellulose (CEL), acid detergent fiber (ADF), neutral detergent fiber (NDF), and in vitro dry matter digestibility (IVDMD) were evaluated in a maize recombinant inbred line (RIL) population.  ADL, CEL, ADF, and NDF gradually increased from 10 to 40 days after silking (DAS), and then they decreased.  IVDMD initially decreased until 40 DAS, and then it increased slightly.  Seventy-two QTLs were identified for the five traits, and each accounted for 3.48–24.04% of the phenotypic variation.  Six QTL hotspots were found, and they were localized in the 1.08, 2.04, 2.07, 7.03, 8.05, and 9.03 bins of the maize genome.  Within the interval of the pleiotropic QTL identified in bin 1.08 of the maize genome, six genes associated with cell wall component biosynthesis were identified as potential candidate genes for stalk strength as well as cell wall-related traits.  In addition, 26 conditional QTLs were detected in the five stages for all of the investigated traits.  Twenty-two of the 26 conditional QTLs were found at 30 DAS conditioned using the values of 20 DAS, and at 50 DAS conditioned using the values of 40 DAS.  These results indicated that cell wall-related traits are regulated by many genes, which are specifically expressed at different stages after silking.  Simultaneous improvements in both forage digestibility and lodging resistance could be achieved by pyramiding multiple beneficial QTL alleles identified in this study.

Agaricus bisporus is one of the most widely cultivated mushrooms in the world. Commercial cultivars are usually phenotypically alike and easy to be copied by isolating tissue cultures. This brings great challenges to distinguish different cultivars and to protect new varieties. Thus, techniques for the accurate identification of cultivars are essentially required. In this study, we accurately identified 11 commercial cultivars of A. bisporus released in China by using microsatellite (SSR, simple sequence repeat) markers. SSR markers were developed by mining the genome sequence. A total of 3 134 SSRs were identified, of which 1 490 SSRs were distributed in gene models, and 1 644 in the intergenic regions. A total of 17 polymorphic primer pairs were developed and SSR fingerprints were constructed for all the commercial cultivars. These SSR markers generated a total of 73 alleles, with an average of 4.29 per locus. Specifically, the primer combination of AB_SSR_2341 and AB_SSR_2590 could distinguish all the 11 commercial cultivars. The similarity coefficients of the 11 commercial cultivars were between 0.56 and 0.95 indicating that some of them were close related. Our results provide an efficient technique for the identification of A. bisporus cultivars in China, which can also facilitate the marker-assisted breeding in the future.