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Combining the critical nitrogen concentration and machine learning algorithms to estimate nitrogen deficiency in rice from UAV hyperspectral data
YU Feng-hua, BAI Ju-chi, JIN Zhong-yu, GUO Zhong-hui, YANG Jia-xin, CHEN Chun-ling
2023, 22 (4): 1216-1229.   DOI: 10.1016/j.jia.2022.12.007
Abstract220)      PDF in ScienceDirect      

Rapid and large area acquisition of nitrogen (N) deficiency status is important for achieving the optimal fertilization of rice.  Most existing studies, however, focus on the use of unmanned aerial vehicle (UAV) remote sensing to diagnose N nutrition in rice, while there are fewer studies on the quantitative description of the degree of N deficiency in rice, and the effects of the critical N concentration on the spectral changes in rice have rarely been explored.  Therefore, based on the canopy spectral data obtained by remotely-sensed UAV hyperspectral images, the N content in rice was obtained through field sampling.  The construction method of the rice curve for the northeastern critical N concentration was studied, and on this basis, N deficiency was determined.  Taking the spectrum of the critical N concentration state as the standard spectrum, the spectral reflectivity data were transformed by the ratios and differences, and the feature extraction of the spectral data was carried out by the successive projections algorithm (SPA).  Finally, by taking the characteristic band as the input variable and N deficiency as the output variable, a set of multivariate linear regression (MLR), long short-term memory (LSTM) inversion models based on extreme learning machine (ELM), and the non-dominated sorting genetic algorithm III extreme learning machine (NSGA-III-ELM) were constructed.  The results showed two key aspects of this system: 1) The correlation between the N deficiency data and original spectrum was poor, but the correlation between the N deficiency data and N deficiency could be improved by a difference change and ratio transformation; 2) The inversion results based on the ratio spectrum and NSGA-III-ELM algorithm were the best, as the R2 values of the training set and validation set were 0.852 and 0.810, and the root mean square error (RMSE) values were 0.291 and 0.308, respectively.  From the perspective of the spectral data, the inversion accuracy of the ratio spectrum was better than the accuracy of the original spectrum or difference spectrum.  At the algorithm level, the model inversion results based on LSTM algorithms showed a serious overfitting phenomenon and poor inversion effect.  The inversion accuracy based on the NSGA-III-ELM algorithm was better than the accuracy of the MLR algorithm or the ELM algorithm.  Therefore, the inversion model based on the ratio spectrum and NSGA-III-ELM algorithm could effectively invert the N deficiency in rice and provide critical technical support for accurate topdressing based on the N status in the rice.

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StOFP20 regulates tuber shape and interacts with TONNEAU1 Recruiting Motif proteins in potato
AI Ju, WANG Ye, YAN Ya-wen, LI Chen-xiao, LUO Wei, MA Ling, SHANG Yi, GAO Dong-li
2023, 22 (3): 752-761.   DOI: 10.1016/j.jia.2022.08.069
Abstract374)      PDF in ScienceDirect      

The OVATE family proteins (OFPs) are plant-specific proteins that modulate diverse aspects of plant growth and development.  In tomato, OFP20 has been shown to interact with TONNEAU1 Recruiting Motif (TRM) proteins to regulate fruit shape.  In this study, we demonstrated that the mutation of StOFP20 caused a shift from round to oval shaped tubers in a diploid accession C151, supporting the role of StOFP20 in controlling tuber shape.  Its expression reached a maximum in the tuber initiation stage and then decreased as the tuber develops.  To help elucidate the mechanism of tuber shape regulation by StOFP20, 27 TONNEAU1 Recruiting Motif (TRM) proteins were identified and 23 of them were successfully amplified in C151.  A yeast two-hybrid assay identified three TRM proteins that interacted with StOFP20, which was confirmed by firefly luciferase complementation in tobacco leaves.  The OVATE domain was indispensable for the interactions, while the necessity of the M10 motif in TRM proteins varied among the interactions between StOFP20 and the three TRMs.  In summary, both StOFP20 and SlOFP20 directed interactions with TRM proteins, but the corresponding interactants were not completely consistent, implying that they exert regulatory roles through mechanisms that are only partially overlapping.  

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Does nitrogen application rate affect the moisture content of corn grains?
ZHANG Yuan-meng, XUE Jun, ZHAI Juan, ZHANG Guo-qiang, ZHANG Wan-xu, WANG Ke-ru, MING Bo, HOU Peng, XIE Rui-zhi, LIU Chao-wei, LI Shao-kun
2021, 20 (10): 2627-2638.   DOI: 10.1016/S2095-3119(20)63401-3
Abstract89)      PDF in ScienceDirect      
Nitrogen fertilizer application is an important measure to obtain high and stable corn yield, and the moisture content of corn grains is an important factor affecting the quality of mechanical grain harvesting.  In this study, four different nitrogen fertilizer treatments from 0 to 450 kg ha–1 pure nitrogen were set for a planting density of 12.0×104 plants ha–1 in 2017 and 2018, and 18 different nitrogen fertilizer treatments from 0 to 765 kg ha–1 pure nitrogen were set for planting densities of 7.5×104 and 12.0×104 plants ha–1 in 2019, to investigate the effect of nitrogen application rate on the moisture content of corn grains.  Under each treatment, the growth of corn, leaf area index (LAI) of green leaves, grain moisture content, and grain dehydration rate were measured.  The results showed that, as nitrogen application increased from 0 to 765 kg ha–1, the silking stage was delayed by about 1 day, the maturity stage was delayed by about 1–2 days, and the number of physiologically mature green leaves and LAI increased.  At and after physiological maturity, the extreme difference in grain moisture content between different nitrogen application rates was 1.9–4.0%.  As the amount of nitrogen application increased, the corn grain dehydration rate after physiological maturity decreased, but it did not reach statistical significance between nitrogen application rate and grain dehydration rate.  No significant correlation was observed between LAI at physiological maturity and grain dehydration rate after physiological maturity.  In short, nitrogen application affected the grain moisture content of corn at and after physiological maturity, however, the difference in grain moisture content among different nitrogen application rates was small.  These results suggest that the effect of nitrogen application on the moisture content of corn grains should not be considered in agricultural production.
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The dynamic impact of income and income distribution on food consumption among adults in rural China
LI Lei, ZHAI Shi-xian, BAI Jun-fei
2021, 20 (1): 330-342.   DOI: 10.1016/S2095-3119(20)63239-7
Abstract170)      PDF in ScienceDirect      
Previous studies have demonstrated that income has a significant effect on food demand in rural China.  However, little research has focused on the dynamic impact of income and income distribution on food demand in rural China.  Using China Health and Nutrition Survey data, this study employs a consistent two-step quadratic almost ideal demand system model, with addressed problems of endogeneity of total expenditure and zero shares, to estimate the food demand elasticities among adults in rural areas with regard to the different income strata.  The results show that changes in income and income strata have significant effects on food demand in rural areas.  Except for grains, all other food groups, including vegetables, oils and fats, animal products, and other foods, have positive income elasticities, and the rise in the income strata will lead to declining income elasticities for grains, vegetables, oils and fats, and
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Exogenous application of a low concentration of melatonin enhances salt tolerance in rapeseed (Brassica napus L.) seedlings
ZENG Liu, CAI Jun-song, LI Jing-jing, LU Guang-yuan, LI Chun-sheng, FU Gui-ping, ZHANG Xue-kun, MA Hai-qing, LIU Qing-yun, ZOU Xi-ling, CHENG Yong
2018, 17 (2): 328-335.   DOI: 10.1016/S2095-3119(17)61757-X
Abstract827)      PDF in ScienceDirect      
Melatonin is a naturally occurring compound in plants.  Here, we tested the effect of exogenous melatonin on rapeseed (Brassica napus L.) grown under salt stress.  Application of 30 μmol L–1 melatonin alleviated salt-induced growth inhibition, and the shoot fresh weight, the shoot dry weight, the root fresh weight, and the root dry weight of seedlings treated with exogenous melatonin increased by 128.2, 142.9, 122.2, and 124.2%, respectively, compared to those under salt stress.  In addition, several physiological parameters were evaluated.  The activities of antioxidant enzymes including peroxidase (POD), catalase (CAT) and ascorbate peroxidase (APX) were enhanced by 16.5, 19.3, and 14.2% compared to their activities in plants without exogenous melatonin application under salt stress, while the H2O2 content was decreased by 11.2% by exogenous melatonin.  Furthermore, melatonin treatment promoted solute accumulation by increasing the contents of proline (26.8%), soluble sugars (15.1%) and proteins (58.8%).  The results also suggested that higher concentrations (>50 μmol L–1) of melatonin could attenuate or even prevent the beneficial effects on seedling development.  In conclusion, application of a low concentration of exogenous melatonin to rapeseed plants under salt stress can improve the H2O2-scavenging capacity by enhancing the activities of antioxidant enzymes such as POD, CAT and APX, and can also alleviate osmotic stress by promoting the accumulation of osmoregulatory substances such as soluble proteins, proline, and water soluble glucan.  Ultimately, exogenous melatonin facilitates root development and improves the biomass of rapeseed seedlings grown under salt stress, thereby effectively alleviating the damage of salt stress in rapeseed seedlings.
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Maize-soybean strip intercropping: Achieved a balance between high productivity and sustainability
DU Jun-bo, HAN Tian-fu, GAI Jun-yi, YONG Tai-wen, SUN Xin, WANG Xiao-chun, YANG Feng, LIU Jiang, SHU Kai, LIU Wei-guo, YANG Wen-yu
2018, 17 (04): 747-754.   DOI: 10.1016/S2095-3119(17)61789-1
Abstract1054)      PDF in ScienceDirect      
Intercropping is one of the most vital practice to improve land utilization rate in China that has limited arable land resource. However, the traditional intercropping systems have many disadvantages including illogical field lay-out of crops, low economic value, and labor deficiency, which cannot balance the crop production and agricultural sustainability. In view of this, we developed a novel soybean strip intercropping model using maize as the partner, the regular maize-soybean strip intercropping mainly popularized in northern China and maize-soybean relay-strip intercropping principally extended in southwestern China. Compared to the traditional maize-soybean intercropping systems, the main innovation of field lay-out style in our present intercropping systems is that the distance of two adjacent maize rows are shrunk as a narrow strip, and a strip called wide strip between two adjacent narrow strips is expanded reserving for the growth of two or three rows of soybean plants.  The distance between outer rows of maize and soybean strips are expanded enough for light use efficiency improvement and tractors working in the soybean strips.  Importantly, optimal cultivar screening and increase of plant density achieved a high yield of both the two crops in the intercropping systems and increased land equivalent ratio as high as 2.2.  Annually alternative rotation of the adjacent maize- and soybean-strips increased the grain yield of next seasonal maize, improved the absorption of nitrogen, phosphorus, and potasium of maize, while prevented the continuous cropping obstacles.  Extra soybean production was obtained without affecting maize yield in our strip intercropping systems, which balanced the high crop production and agricultural sustainability.
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Significant association of the novel Rf4-targeted SNP marker with the restorer for WA-CMS in different rice backgrounds and its utilization in molecular screening
CHEN Li-kai, YAN Xian-cheng, DAI Jun-hao, CHEN Si-ping, LIU Yong-zhu, WANG Hui, CHEN Zhiqiang, GUO Tao
2017, 16 (10): 2128-2135.   DOI: 10.1016/S2095-3119(16)61620-9
Abstract785)      PDF in ScienceDirect      
   In the rice cytoplasmic-genetic male sterility (CMS) system, the combination of a CMS line, maintainer line and restorer line carrying the restorer gene to restore fertility, is indispensable for the development of hybrids. However, the process of screening for the trait of fertility restoration is laborious and time-consuming. In the present study, we analyzed the nucleotide sequence of the Rf4 gene, which is the major locus controlling fertility restoration, to identify allele-specific variation. A single nucleotide polymorphism (SNP) A/C at +474 in the coding sequence (CDS) was found to be capable of strictly distinguishing groups of alleles Rf4 (A) and rf4 (C). Using KASP genotyping, this valuable SNP was converted to an allele-specific PCR marker. We evaluated and validated the marker among three-line parents with different backgrounds, and the results revealed a complete correlation between SNP alleles and the fertility restoration phenotype. Molecular screening was subsequently carried out for the presence of alleles of Rf4 and Rf3 among 328 diverse rice cultivars with worldwide distribution. The results demonstrate that this SNP marker could be the optimal choice for the molecular identification of potential restorers.
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Food packing: A case study of dining out in Beijing
WANG Yu, XU Shi-wei, YU Wen, Ahmed Abdul-gafar, LIU Xiao-jie, BAI Jun-fei, ZHANG Dan, GAO Liwei, CAO Xiao-chang, LIU Yao
2016, 15 (8): 1924-1931.   DOI: 10.1016/S2095-3119(15)61282-5
Abstract1892)      PDF in ScienceDirect      
  Food waste results in nutritional losses, ecological damage, and environmental pollution. This survey is conducted in Beijing and aims to determine whether food waste can be reduced by food packing when leftovers are produced at the dining table and to identify factors that affect food packing behavior and the use of leftovers. Based on statistical and econometric analyses of the relationship between leftovers packing and possible factors, this study finds that the age, educational level, employment status, farming experience, environmental protection consciousness, food saving advertisement, families with old members, and reasons for dining out significantly influence the food packing behavior of the consumers. Moreover, the dining environment plays an important role in leftovers packing. People with intimate relationships, such as families, friends, classmates, or colleagues, are more willing to take leftovers home. Business partners do the opposite. Finally, almost all packed leftovers (91.59%) are eaten by people and animals. Therefore, packing leftovers is an excellent approach to reduce food waste.
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Demographics, societal aging, and meat consumption in China
MIN Shi, BAI Jun-fei, James Seale Jr., Thomas Wahl
2015, 14 (6): 995-1007.   DOI: 10.1016/S2095-3119(14)60984-9
Abstract1854)      PDF in ScienceDirect      
Drawn on the data collected by surveying 1340 urban households from six cities in China, this paper estimates the impacts of demographic structure and population aging on household meat consumption, by jointly considering meat consumed at home and away from home. Based on the trajectories of population, a simple simulation on meat demand trend in China is conducted subsequently. The results suggest: 1) Meat consumed away from home averagely accounts for near 30% of household total meat consumption in terms of quantity, so that its omission likely leads to a significant underestimate of total meat consumption and misunderstanding the driving forces; 2) population aging significantly and negatively affects per capita meat consumption, suggesting that the expected meat demand in China without considering population aging will be overestimated. The findings from this study have important implications for better understanding the relative issues on China’s meat consumption under the situation of population aging.
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Direct farm, production base, traceability and food safety in China
DING Ji-ping, HUANG Ji-kun, JIA Xiang-ping, BAI Jun-fei, Steve Boucher, Michael Carter
2015, 14 (11): 2380-2390.   DOI: 10.1016/S2095-3119(15)61127-3
Abstract1713)      PDF in ScienceDirect      
With the rapid growth of China’s economy, rising demand for safety food has been accompanied by frequent food safety scandals. Given that China’s farming is dominated by millions of small-scale farms, ensuring food safety is a major challenge facing the public and private sectors. The direct farm (DF) program, initiated in 2008, represents one of the government’s major initiatives to modernize the distribution of fresh fruit and vegetables (FFV) and improve food safety. Under the DF program, participating national and international retailers are expected to establish more direct procurement relationships with farm communities. While it is often claimed that greater participation by retailers in the production and post-harvest processing implied the DF program will lead to improved quality, safety and traceability, systematic evidence remains elusive as existing studies are largely narrative, based on case studies, or theoretical inference. Little empirical evidence is available for a broader evaluation of the DF program. This paper aims to fill this gap by assessing the overall performance of a single retailer’s DF experience with respect to the procurement and food safety of FFV. We use data from a survey of production managers of 35 DF production bases (PBs) spread across 11 provinces, 3 cities and 1 autonomous region in China. The results show a mixture of opportunities and challenges. On one hand, the DF program improves production practices and distribution channels of FFV produced on its PBs, thus facilitating the move of China’s food system towards improved food safety compliance. On the other hand, significant heterogeneity in the traceability of food and the ability of DF to meet higher safety standards is evident both across major product categories and across household-operated vs. firm-operated PBs. The paper concludes with policy implications.
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Genetic Diversity of Chinese Soybean mosaic virus Strains and Their Relationships with Other Plant Potyviruses Based on P3 Gene Sequences
YANG Qing-hua, LI Kai, ZHI Hai-jian , GAI Jun-yi
2014, 13 (10): 2184-2195.   DOI: 10.1016/S2095-3119(13)60653-X
Abstract1125)      PDF in ScienceDirect      
Soybean mosaic virus (SMV), a member of the genus Potyvirus, is a major pathogen of soybean plants in China, and 16 SMV strains have been identified nationwide based on a former detailed SMV classification system. As the P3 gene is thought to be involved in viral replication, systemic infection, pathogenicity, and overcoming resistance, knowledge of the P3 gene sequences of SMV and other potyviruses would be useful in efforts to know the genetic relationships among them and control the disease. P3 gene sequences were obtained from representative isolates of the above-mentioned 16 SMV strains and were compared with other SMV strains and 16 Potyvirus species from the National Center for Biotechnology GenBank database. The P3 genes from the 16 SMV isolates are composed of 1 041 nucleotides, encoding 347 amino acids, and share 90.7-100% nucleotide (NT) sequence identities and 95.1-100% amino acid (AA) sequence identities. The P3 coding regions of the 16 SMV isolates share high identities (92.4-98.9% NT and 96.0-100% AA) with the reported Korean isolates, followed by the USA isolates (88.5-97.9% NT and 91.4-98.6% AA), and share low identities (80.5-85.2% NT and 82.1-84.7% AA) with the reported HZ1 and P isolates from Pinellia ternata. The sequence identities of the P3 genes between SMV and the 16 potyviruses varied from 44.4 to 81.9% in the NT sequences and from 21.4 to 85.3% in the AA sequences, respectively. Among them, SMV was closely related to Watermelon mosaic virus (WMV), with 76.0-81.9% NT and 77.5-85.3% AA identities. In addition, the SMV isolates and potyvirus species were clustered into six distinct groups. All the SMV strains isolated from soybean were clustered in Group I, and the remaining species were clustered in other groups. A multiple sequence alignment analysis of the C-terminal regions indicated that the P3 genes within a species were highly conserved, whereas those among species were relatively variable.
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QTL Identification of the Insensitive Response to Photoperiod and Temperature in Soybean by Association Mapping
ZUO Qiao-mei, WEN Zi-xiang, ZHANG Shu-yun, HOU Jin-feng, GAI Jun-yi, YU De-yue , XING Han
2013, 12 (8): 1423-1430.   DOI: 10.1016/S2095-3119(13)60554-7
Abstract1194)      PDF in ScienceDirect      
The insensitive response to photoperiod and temperature is an important quantitative trait for soybean in wide adaptation breeding. The natural variation in response to photoperiod and temperature was detected using 275 accessions of soybean [Glycine max (L.) Merrill] from China. Genome-wide association mapping, based on population structure analysis, was carried out using 118 SSR markers by the TASSEL GLM (general linear model) program. Nine SSR markers (P<0.01) were associated with the value of the response to photoperiod and temperature (VRPT) caused by days to flowering (DF), among which, Satt308 (LG M), Satt150 (LG M) and Satt440 (LG I), were identified in both 2006 and 2007. Twelve SSR markers (P<0.01) were associated with VRPT caused by days to maturity (DM), among which three markers, Satt387 (LG N), Satt307 (LG C2) and AW310961 (LG J), were detected in both 2006 and 2007. In addition, a total of 20 elite alleles were screened out over 2006 and 2007 for being associated with an insensitive response to photoperiod and temperature (IRPT) caused by DF and a total of seven different elite alleles were screened out for being associated with IRPT caused by DM. Among these elite alleles, five alleles, Satt150-244, Satt308-164, Satt308-206, Satt440-176, and Satt440-206, were associated with IRPT caused by DF and were identified in both years, but only one allele, Satt307-170, was identified as being associated with an IRPT caused by DM. Based on these elite alleles, a set of typical accessions were screened out. The result about the genetic basis of IRPT is meaningful for soybean wide adaption breeding.
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Cloning and Characterization of a Novel Gene GmMF1 in Soybean (Glycine max L. Merr.)
JIANG Wei, YANG Shou-ping, YU De-yue and GAI Jun-yi
2011, 10 (12): 1834-1841.   DOI: 10.1016/S1671-2927(11)60183-1
Abstract1700)      PDF in ScienceDirect      
Cytoplasmic male sterility plays an important role in utilization of crop heterosis. Screening of soybean for novel genes related to male sterility in soybean could provide a basis for studying the molecular mechanism of male sterility in plants. In this study, gene differential expressions between the cytoplasmic male-sterile line NJCMS1A and its maintainer line NJCMS1B in soybean were analyzed using cDNA-AFLP. A differentially expressed fragment, GmMF-T4A15, was isolated from large flower buds of NJCMS1B. By searching the soybean genomic library and PCR amplification, the cDNA fulllength sequence of 1 311 bp was obtained and named GmMF1. The expression characteristics of GmMF1 were studied by semiquantitative real-time PCR and real-time quantitative PCR. The results showed that GmMF1 was expressed highly in flower buds of NJCMS1B. The deduced protein contains 436 amino acids and shows high similarity to members of the DUF620 protein family with unknown functions in other plant species. It is predicted that the protein encoded by GmMF1 is localized in the nucleus.
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Identification, Genetic Analysis and Mapping of Resistance to Phytophthora sojae of Pm28 in Soybean
WU Xiao-ling, ZHANG Bao-qiang, SUN Shi, ZHAO Jin-ming, YANG Feng, GUO Na, GAI Jun-yi, XING Han
2011, 10 (10): 1506-1511.   DOI: 10.1016/S1671-2927(11)60145-4
Abstract2145)      PDF in ScienceDirect      
Phytophthora sojae Kanfman and Gerdemann (P. sojae) is one of the most prevalent pathogens and causes Phytophthora root rot, which limits soybean production worldwide. Development of resistant cultivars is a cost-effective approach to controlling this disease. In this study, 127 soybean germplasm were evaluated for their responses to Phytophthora sojae strain Pm28 using the hypocotyl inoculation technique, and 49 were found resistant to the strain. The hypocotyl of P1, P2, F1, and F2:3 of two crosses of Ludou 4 (resistant)×Youchu 4 (susceptible) and Cangdou 5 (resistant)×Williams (susceptible) were inoculated with Pm28, and were used to analyze the inheritance of resistance. The population derived from the cross of Ludou 4×Youchu 4 was used to map the resistance gene (designated as Rps9) to a linkage group. 932 pairs of SSR primers were used to detect polymorphism, and seven SSR markers were mapped near the resistance gene. The results showed that the resistance to Pm28 in Ludou 4 and Cangdou 5 was controlled by a single dominant gene Rps9, which was located on the molecular linkage group N between the SSR markers Satt631 (7.5 cM) and Sat_186 (4.3 cM).
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