The genome evolution and domestication of tropical fruit mango

Background: Mango is one of the world’s most important tropical fruits. It belongs to the family Anacardiaceae, which includes several other economically important species, notably cashew, sumac and pistachio from other genera. Many species in this family produce family-specific urushiols and related phenols, which can induce contact dermatitis. Results: We generate a chromosome-scale genome assembly of mango, providing a reference genome for the Anacardiaceae family. Our results indicate the occurrence of a recent whole-genome duplication (WGD) event in mango. Duplicated genes preferentially retained include photosynthetic, photorespiration, and lipid metabolic genes that may have provided adaptive advantages to sharp historical decreases in atmospheric carbon dioxide and global temperatures. A notable example of an extended gene family is the chalcone synthase (CHS) family of genes, and particular genes in this family show universally higher expression in peels than in flesh, likely for the biosynthesis of urushiols and related phenols. Genome resequencing reveals two distinct groups of mango varieties, with commercial varieties clustered with India germplasms and demonstrating allelic admixture, and indigenous varieties from Southeast Asia in the second group. Landraces indigenous in China formed distinct clades, and some showed admixture in genomes. Conclusions: Analysis of chromosome-scale mango genome sequences reveals photosynthesis and lipid metabolism are preferentially retained after a recent WGD event, and expansion of CHS genes is likely associated with urushiol biosynthesis in mango. Genome resequencing clarifies two groups of mango varieties, discovers allelic admixture in commercial varieties, and shows distinct genetic background of landraces

The genome evolution and domestication of tropical fruit mango

Background: Mango is one of the world’s most important tropical fruits. It belongs to the family Anacardiaceae, which includes several other economically important species, notably cashew, sumac and pistachio from other genera. Many species in this family produce family-specific urushiols and related phenols, which can induce contact dermatitis. Results: We generate a chromosome-scale genome assembly of mango, providing a reference genome for the Anacardiaceae family. Our results indicate the occurrence of a recent whole-genome duplication (WGD) event in mango. Duplicated genes preferentially retained include photosynthetic, photorespiration, and lipid metabolic genes that may have provided adaptive advantages to sharp historical decreases in atmospheric carbon dioxide and global temperatures. A notable example of an extended gene family is the chalcone synthase (CHS) family of genes, and particular genes in this family show universally higher expression in peels than in flesh, likely for the biosynthesis of urushiols and related phenols. Genome resequencing reveals two distinct groups of mango varieties, with commercial varieties clustered with India germplasms and demonstrating allelic admixture, and indigenous varieties from Southeast Asia in the second group. Landraces indigenous in China formed distinct clades, and some showed admixture in genomes. Conclusions: Analysis of chromosome-scale mango genome sequences reveals photosynthesis and lipid metabolism are preferentially retained after a recent WGD event, and expansion of CHS genes is likely associated with urushiol biosynthesis in mango. Genome resequencing clarifies two groups of mango varieties, discovers allelic admixture in commercial varieties, and shows distinct genetic background of landraces

Mitigated Greenhouse Gas Emissions in Cropping Systems by Organic Fertilizer and Tillage Management

Cultivating ecological benefits in agricultural systems through greenhouse gas emission reduction will offer extra economic benefits for farmers. The reported studies confirmed that organic fertilizer application could promote soil carbon sequestration and mitigate greenhouse gas emissions under suitable tillage practices in a short period of time. Here, a field experiment was conducted using a two-factor randomized block design (organic fertilizers and tillage practices) with five treatments. The results showed that the application of microbial fertilizers conserved soil heat and moisture, thereby significantly reducing CO2 emissions (6.9–18.9%) and those of N2O and CH4 fluxes during corn seasons, compared with chemical fertilizer application. Although deep tillage increased total CO2 emissions by 4.9–37.7%, it had no significant effect on N2O and CH4 emissions. Application of microbial organic fertilizer increased corn yield by 21.5%, but it had little effect on the yield of wheat. Overall, application of microbial fertilizers significantly reduced soil GHG emission and concurrently increased yield under various tillage practices in a short space of time. With this, it was critical that microbial fertilizer be carefully studied for application in wheat–corn cropping systems

Mitigated Greenhouse Gas Emissions in Cropping Systems by Organic Fertilizer and Tillage Management

Cultivating ecological benefits in agricultural systems through greenhouse gas emission reduction will offer extra economic benefits for farmers. The reported studies confirmed that organic fertilizer application could promote soil carbon sequestration and mitigate greenhouse gas emissions under suitable tillage practices in a short period of time. Here, a field experiment was conducted using a two-factor randomized block design (organic fertilizers and tillage practices) with five treatments. The results showed that the application of microbial fertilizers conserved soil heat and moisture, thereby significantly reducing CO2 emissions (6.9–18.9%) and those of N2O and CH4 fluxes during corn seasons, compared with chemical fertilizer application. Although deep tillage increased total CO2 emissions by 4.9–37.7%, it had no significant effect on N2O and CH4 emissions. Application of microbial organic fertilizer increased corn yield by 21.5%, but it had little effect on the yield of wheat. Overall, application of microbial fertilizers significantly reduced soil GHG emission and concurrently increased yield under various tillage practices in a short space of time. With this, it was critical that microbial fertilizer be carefully studied for application in wheat–corn cropping systems

Anti-Inflammatory Effect of Geniposide on Osteoarthritis by Suppressing the Activation of p38 MAPK Signaling Pathway

It has been suggested that the activation of the p38 mitogen activated protein kinases (MAPKs) signaling pathway plays a significant role in the progression of OA by leading to the overexpression of proinflammatory cytokines, chemokines, and signaling enzymes in human osteoarthritis chondrocytes. However, most p38 MAPK inhibitors applied for OA have been thought to be limited due to their potential long-term toxicities. Geniposide (GE), an iridoid glycoside purified from the fruit of the herb, has been widely used in traditional medicine for the treatment of a variety of chronic inflammatory diseases. In this study, we evaluated the inhibition effect of geniposide on the inflammatory progression of the surgically induced osteoarthritis and whether the protective effect of geniposide on OA is related to the inhibition of the p38 MAPK signaling pathway. In vitro, geniposide attenuated the expression of inflammatory cytokines including interleukin-1 (IL-1), tumor necrosis factor (TNF-α), and nitric oxide (NO) production as well as matrix metalloproteinase- (MMP-) 13 in chondrocytes isolated from surgically induced rabbit osteoarthritis model. Additionally, geniposide markedly suppressed the expression of IL-1, TNF-α, NO, and MMP-13 in the synovial fluid from the rabbits with osteoarthritis. More importantly, our results clearly demonstrated that the inhibitory effect of geniposide on surgery-induced expression of inflammatory mediators in osteoarthritis was closely associated with the suppression of the p38 MAPK signaling pathways. Our study demonstrates that geniposide may have therapeutic potential to serve as an alternative agent for the p38 MAPK inhibition for the treatment of OA due to its inherent features of biological activities and low toxicity as a traditional Chinese medicine

Increase in Soil Carbon Pool Stability Rather Than Its Stock in Coastal Saline—Alkali Ditches following Reclamation Time

Extensive drainage ditches are constructed to reduce soil salinity in reclaimed saline–alkali farmland, consequently forming plant growth hotspots and impacting soil carbon stocks therein. However, the investigation into changes in soil carbon stocks remains limited in these ditches. To address this, soil samples were collected from drainage ditches, which originated from the reclamation of saline–alkali farmland, at different reclamation years (the first, seventh, and fifteenth year). Moreover, fractions were separated from soil samples; a particle size separation method (particulate organic matter, POM; mineral–associated organic matter, MAOM) and a spatio–temporal substitution method were conducted to analyze the variations in soil carbon components and the underlying mechanisms. The results indicate that there were no significant variations in the contents and stocks of soil organic carbon (SOC) and soil inorganic carbon (SIC) following the increase in reclamation time. However, in the POM fraction, the SOC content (SOCPOM) and stock significantly decreased from 2.24 to 1.12 g kg−1 and from 19.02 to 12.71 Mg ha−1, respectively. Conversely, in the MAOM fraction, the SOC content (SOCMAOM) and stock significantly increased from 0.65 to 1.70 g kg−1 and from 5.30 to 12.27 Mg ha−1, respectively. The different changes in SOCPOM and SOCMAOM, as well as the result of the structural equation model, showed a possible transformation process from SOCPOM to SOCMAOM in the soil carbon pool under the driving force of reclamation time. The results in terms of the changes in soil carbon components demonstrate the stability rather than the stock of the soil carbon pool increase in coastal saline–alkali ditches following the excavation formation time. Although more long time series and direct evidence are needed, our findings further provide a case study for new knowledge about changes in the soil carbon pool within saline–alkali ditches and reveal the potential processes involved in the transformation of soil carbon components

Soil Microbes from Saline–Alkali Farmland Can Form Carbonate Precipitates

The formation of soil inorganic carbon in saline–alkali lands is of great significance for enhancing soil carbon sequestration. As for the formation mechanisms, in addition to the discovered abiotic mechanisms, the microbial mechanisms remain unclear. To address this, soil microbes were isolated from the saline–alkali farmland of the Yellow River Delta in north China. Then, their capacity for carbonate precipitation formation was determined. Ten microbial strains were obtained from the soil. Of these, seven strains (four bacterial strains and three fungal strains), belonging to Rhodococcus sp., Pseudomonas sp., Bacillus sp., Streptomyces sp., Aspergillus sp., Cladosporium sp., and Trichoderma sp., formed carbonate precipitates in the range of 89.77~383.37 mg. Moreover, the formation of carbonate precipitates was related to specific metabolisms by which microbes can raise the pH (from 7.20 to >8.00), suggesting that soil microbes that can enhance pH values by specific metabolisms containing the function of carbonate formation. Although an in situ experiment is needed to confirm such capacity, these results showed that soil bacteria and fungi existing in the saline–alkali farmland soil can form carbonate precipitates. The present study provided a microbial perspective for the mechanism of soil inorganic carbon formation, further implying a microbial potential of soil carbon sequestration in saline–alkali farmlands

Soil Microbes from Saline–Alkali Farmland Can Form Carbonate Precipitates

The formation of soil inorganic carbon in saline–alkali lands is of great significance for enhancing soil carbon sequestration. As for the formation mechanisms, in addition to the discovered abiotic mechanisms, the microbial mechanisms remain unclear. To address this, soil microbes were isolated from the saline–alkali farmland of the Yellow River Delta in north China. Then, their capacity for carbonate precipitation formation was determined. Ten microbial strains were obtained from the soil. Of these, seven strains (four bacterial strains and three fungal strains), belonging to Rhodococcus sp., Pseudomonas sp., Bacillus sp., Streptomyces sp., Aspergillus sp., Cladosporium sp., and Trichoderma sp., formed carbonate precipitates in the range of 89.77~383.37 mg. Moreover, the formation of carbonate precipitates was related to specific metabolisms by which microbes can raise the pH (from 7.20 to >8.00), suggesting that soil microbes that can enhance pH values by specific metabolisms containing the function of carbonate formation. Although an in situ experiment is needed to confirm such capacity, these results showed that soil bacteria and fungi existing in the saline–alkali farmland soil can form carbonate precipitates. The present study provided a microbial perspective for the mechanism of soil inorganic carbon formation, further implying a microbial potential of soil carbon sequestration in saline–alkali farmlands

Effects of Different Fertilizers on Rhizosphere Bacterial Communities of Winter Wheat in the North China Plain

The application of bioorganic fertilizer affects rhizosphere microbes and further improves soil fertility in farmlands. However, the effects of different fertilizers on rhizosphere bacterial community diversity and structure of winter wheat remains unclear. In this study, we explored the effects of different fertilization treatments (no fertilizer added, CK; nitrogen fertilizer, NF; bioorganic fertilizer, BOF) on the rhizosphere bacterial community of winter wheat in the North China Plain. Rhizosphere soil treated with BOF had a higher Shannon index than that of CK and NF. The relative abundance of the Proteobacteria treated with BOF was significantly higher than that of NF, while the Acidobacteria and Planctomycetes were significantly lower. The redundancy analysis (RDA) and Mantel test showed that soil bacterial communities were significantly correlated with pH, nitrate, available phosphorus (AP), and available potassium (AK). Our findings indicated that BOF increased bacterial diversity and the relative abundance of copiotrophic bacteria in rhizosphere soil, while NF reduced bacterial diversity and increased the relative abundance of oligotrophic bacteria. The increase in copiotrophic bacteria in the rhizosphere of winter wheat could indicate an increase in soil nutrient availability, which might have positive implications for soil fertility and crop production

An Optimization Scheme of Balancing GHG Emission and Income in Circular Agriculture System

With the rapid development of circular agriculture in China, balancing agricultural income and environmental impact by adjusting the structure and scale of circular agriculture is becoming increasingly important. Agriculture is a major source of greenhouse gas and income earned from agriculture drives sustainable agricultural development. This paper built a multi-objective linear programming model based on greenhouse gas emission and agricultural product income and then optimized the structure and scale of circular agriculture using Beiqiu Farm as a case study. Results showed that greenhouse gas emission was mainly from manure management in livestock industry. While the agriculture income increased by 64% after optimization, GHG emission increased by only 12.3%. The optimization made full use of straw, manure and fodder, but also minimized soil nitrogen loss. The results laid a generalized guide for adjusting the structure and scale of the planting and raising industry. Measures for optimizing the management of manure were critical in achieving low agricultural carbon emissions in future agricultural development efforts