Genome-wide association study and high-quality gene mining related to soybean protein and fat.

BACKGROUND: Soybean is one of the most important oil crops in the world, and its protein and fat are the primary sources of edible oil and vegetable protein. The effective components in soybean protein and fat have positive effects on improving human immunity, anti-tumor, and regulating blood lipids and metabolism. Therefore, increasing the contents of protein and fat in soybeans is essential for improving the quality of soybeans. RESULTS: This study selected 292 soybean lines from different regions as experimental materials, based on SLAF-seq sequencing technology, and performed genome-wide association study (GWAS) on the phenotype data from 2019-2021 Planted at the experimental base of Jilin Agricultural University, such as the contents of protein and fat of soybeans. Through the GLM model and MLM model, four SNP sites (Gm09_39012959, Gm12_35492373, Gm16_9297124, and Gm20_24678362) that were significantly related to soybean fat content were associated for three consecutive years, and two SNP sites (Gm09_39012959 and Gm20_24678362) that were significantly related to soybean protein content were associated. By the annotation and enrichment of genes within the 100 Kb region of SNP loci flanking, two genes (Glyma.09G158100 and Glyma.09G158200) related to soybean protein synthesis and one gene (Glyma.12G180200) related to lipid metabolism were selected. By the preliminary verification of expression levels of genes with qPCR, it is found that during the periods of R6 and R7 of the accumulation of soybean protein and fat, Glyma.09G158100 and Glyma.09G158200 are positive regulatory genes that promote protein synthesis and accumulation, while Glyma.12G180200 is the negative regulatory gene that inhibits fat accumulation. CONCLUSIONS: These results lay the basis for further verifying the gene function and studying the molecular mechanisms regulating the accumulation of protein and fat in soybean seeds.

CH4 and CO2 emissions in water networks of rice cultivation regions.

Rice cultivation regions have a high density of open water networks to meet the requirements of rice growth and production. These open water networks have a significant risk of carbon (C) emissions due to agricultural production, but the C emissions from these waters are not clearly recorded in previous studies. Therefore, this study aimed to explore the pattern and internal mechanism of methane (CH4) and carbon dioxide (CO2) emissions from multiple types of waters (i.e., river, fish pond, reservoir, and ditch) in a typical rice cultivation region in southwestern China. The annual CH4 and CO2 fluxes were higher in the downstream river (2.79-94.89 and 39.39-1699.98 mg m-2 h-1) and ditch (8.80-74.99 and 123.43-542.65 mg m-2 h-1, respectively) and lower in the reservoir (-0.67 to 3.45 and -239.15 to 141.50 mg m-2 h-1) (P < 0.05). The monthly trends of CH4 and CO2 fluxes from the middle river and ditch were driven by interactive reactions of rice cultivation practices and precipitation. In contrast, the emission patterns of CH4 and CO2 from the lower river, upper river, and fish pond were mainly driven by domestic sewage discharge, precipitation, and aquaculture practices, respectively. This study suggested that river and ditch were more sensitive to C emissions than other waters, and the rice production period was the critical period for controlling C emission. Although rice paddy soils yield more cumulative emissions of CH4, water networks in rice cultivation regions were possible hotspots for C emissions due to the higher emission intensities, which were largely overlooked before. Thus, it is necessary to refine and promote practices to better mitigate C emissions from waters in rice cultivation regions in the future.

Visualizing and Understanding Shrinking Cities and Towns (SCT) Research: A Network Analysis.

The world is undergoing an unprecedented trend of fast urbanization, which causes a range of socio-environmental consequences, one of which is shrinking cities and towns (SCT). SCT refer to the cities or towns that are experiencing population decline and economic downturn. In the existing literature, there have been numerous studies on SCT; however, there is a lack of study which investigates its knowledge domains. Therefore, this paper aims to conduct a scientometric analysis to achieve an outline of the SCT research status. Through the procedures of literature search and screening, a total of 716 SCT-related studies were extracted from the Scopus. The VOSviewer software system program was then utilized to visualize the present SCT-related studies. The visualization results revealed that the journal of Sustainability made significant contributions to the SCT research in terms of relevant publications. In addition, Haase, Annegret received the most co-citations, and was also the most productive author in this field. Furthermore, it was identified that current SCT research is mainly conducted in developed countries. Through the analysis of keywords, the emerging research topics were revealed. Discussions were further made from the perspectives of prevailing research methods, evaluation criteria, and solutions for SCT problems.

Fine Mapping and Functional Research of Key Genes for Photoperiod Sensitivity in Maize.

Maize is native to the tropics and is very sensitive to photoperiod. Planting in temperate regions with increased hours of daylight always leads to late flowering, sterility, leggy plants, and increased numbers of maize leaves. This phenomenon severely affects the utilization of tropical maize germplasm resources. The sensitivity to photoperiod is mainly reflected in differences in plant height (PH), ear height (EH), total leaf number (LN), leaf number under ear (LE), silking stage (SS), and anthesis stage (AT) in the same variety under different photoperiod conditions. These differences are more pronounced for varieties that are more sensitive to photoperiod. In the current study, a high-density genetic map was constructed from a recombinant inbred line (RIL) population containing 209 lines to map the quantitative trait loci (QTL) for photoperiod sensitivity of PH, EH, LN, LE, SS, and AT. A total of 39 QTL were identified, including three consistent major QTL. We identified candidate genes in the consensus major QTL region by combined analysis of transcriptome data, and after enrichment by GO and KEGG, we identified a total of four genes (Zm00001d006212, Zm00001d017241, Zm00001d047761, and Zm00001d047632) enriched in the plant circadian rhythm pathway (KEGG:04712). We analyzed the expression levels of these four genes, and the analysis results showed that there were significant differences in response under different photoperiod conditions for three of them (Zm00001d047761, Zm00001d006212 and Zm00001d017241). The results of functional verification showed that the expression patterns of genes rhythmically oscillated, which can affect the length of the hypocotyl and the development of the shoot apical meristem. We also found that the phenotypes of the positive plants were significantly different from the control plants when they overexpressed the objective gene or when it was knocked out, and the expression period, phase, and amplitude of the target gene also shifted. The objective gene changed its own rhythmic oscillation period, phase, and amplitude with the change in the photoperiod, thereby regulating the photoperiod sensitivity of maize. These results deepen our understanding of the genetic structure of photoperiod sensitivity and lay a foundation for further exploration of the regulatory mechanism of photoperiod sensitivity.

Maize plant architecture trait QTL mapping and candidate gene identification based on multiple environments and double populations.

BACKGROUND: The plant architecture traits of maize determine the yield. Plant height, ear position, leaf angle above the primary ear and internode length above the primary ear together determine the canopy structure and photosynthetic efficiency of maize and at the same time affect lodging and disease resistance. A flat and tall plant architecture confers an obvious advantage in the yield of a single plant but is not conducive to dense planting and results in high rates of lodging; thus, it has been gradually eliminated in production. Although using plants that are too compact, short and density tolerant can increase the yield per unit area to a certain extent, the photosynthetic efficiency of such plants is low, ultimately limiting yield increases. Genetic mapping is an effective method for the improvement of plant architecture to identify candidate genes for regulating plant architecture traits. RESULTS: To find the best balance between the yield per plant and the yield per unit area of maize, in this study, the F2:3 pedigree population and a RIL population with the same male parent were used to identify QTL for plant height (PH), ear height (EH), leaf angle and internode length above the primary ear (LAE and ILE) in Changchun and Gongzhuling for 5 consecutive years (2016-2020). A total of 11, 13, 23 and 13 QTL were identified for PH, EH, LAE, and ILE, respectively. A pleiotropic consistent QTL for PH overlapped with that for EH on chromosome 3, with a phenotypic variation explanation rate from 6.809% to 21.96%. In addition, there were major consistent QTL for LAE and ILE, and the maximum phenotypic contribution rates were 24.226% and 30.748%, respectively. Three candidate genes were mined from the three consistent QTL regions and were involved in the gibberellin-activated signal pathway, brassinolide signal transduction pathway and auxin-activated signal pathway, respectively. Analysis of the expression levels of the three genes showed that they were actively expressed during the jointing stage of vigorous maize growth. CONCLUSIONS: In this study, three consistent major QTL related to plant type traits were identified and three candidate genes were screened. These results lay a foundation for the cloning of related functional genes and marker-assisted breeding of related functional genes.

Physical interpretation of shear-rate behaviour of soils and geotechnical solution to the coefficient of start-up friction with low inertial number.

Shear experiments on soils have revealed the effects of shear rate, confining pressure, and grain size on the residual shear strength, but their nature is not well understood. To interpret these behaviours, a single dimensionless inertial number I from granular physics is introduced. A linear relationship between coefficient of residual friction µr and the natural logarithm of I was found by analysing geotechnical test data from other literature and helps to resolve the µ(aI)-rheology, which was proved invalid in the quasi-static regime. A method is proposed that introduces two three-dimensional yield criteria for soils to classify the frictional properties between grains in the quasi-static regime. The empirical coefficient of start-up friction is replaced by strength parameters of the soil. When compliant with the Mohr-Coulomb yield criterion, this coefficient is positively correlated with the internal angle of friction but negatively correlated with the Lode angle. Moreover from further analysis, the calculated strength is smallest in the pure tension state, largest in the pure compression state, and intermediate in the pure shearing state. This result is consistent with the properties of compressive endurable and tensive intolerable for natural geomaterials.

Wet nitrogen deposition across the urban-intensive agricultural-rural transect of a small urban area in southwest China.

Understanding of the spatial and temporal variation of the flux of atmospheric nitrogen (N) deposition is essential for assessment of its impact on ecosystems. However, little attention has been paid to the variability of N deposition across urban-intensive agricultural-rural transects. A continuous 2-year observational study (from January 2015 to December 2016) was conducted to determine wet N deposition across the urban-intensive agricultural-rural transect of a small urban area in southwest China. Significantly spatial and temporal variations were found in the research area. Along the urban-intensive agricultural-rural transect, the TN and NH4+-N deposition first increased and then decreased, and the NO3--N and dissolved organic N (DON) deposition decreased continuously. Wet N deposition was mainly affected by the districts of agro-facilities, roads and build up lands. Wet NH4+-N deposition had non-seasonal emission sources including industrial emissions and urban excretory wastes in urban districts and seasonal emission sources such as fertilizer and manure volatilization in the other districts. However, wet NO3--N deposition had seasonal emission sources such as industrial emissions and fireworks in urban district and non-seasonal emission sources such as transportation in the other districts. Deposition of DON was likely to have had similar sources to NO3--N deposition in rural district, and high-temperature-dependent sources in urban and intensive agricultural districts. Considering the annual wet TN deposition in the intensive agricultural district was about 11.1% of the annual N fertilizer input, N fertilizer rates of crops should be reduced in this region to avoid the excessive application, and the risk of N emissions to the environment.