Search Result

Select

Identification of key genes and metabolites involved in meat quality performance in Qinchuan cattle by WGCNA

Hengwei Yu, Zhimei Yang, Jianfang Wang, Huaxuan Li, Xuefeng Li, Entang Liang, Chugang Mei, Linsen Zan

2024, 23 (11): 3923-3937. DOI: 10.1016/j.jia.2024.07.044

Abstract （97） PDF in ScienceDirect

Understanding the genetic and metabolic elements that impact meat quality is crucial to improving production and meeting consumer demands in the beef sector. Differences in meat quality among various muscle areas in beef cattle can impact pricing in the market. Despite progress in genomics, the specific genes and metabolites that affect meat quality characteristics in Qinchuan cattle remain inadequately understood. Therefore, this study aims to evaluate the meat quality characteristics of four specific muscle locations (tenderloin, striploin, high rib, and ribeye muscles) in Qinchuan bulls, including 10 traits (total protein content (TPC), intramuscular fat (IMF), non-esterified fatty acid (NEFA), meat color (L*, a*, and b*), shear force (SF), cooking loss (CL), pH₀, and pH₂₄). This experiment uses transcriptome, metabolome sequencing, and sophisticated analytical methodologies such as weighted gene co-expression network analysis (WGCNA) and protein–protein interaction networks (PPI) to identify the key genes and metabolites associated with specific traits. The findings highlight three notable genes (NDUFAB1, NDUFA12, and NDUFB7) linked to intramuscular fat (IMF), three key genes (CSRP3, ACAA3, and ACADVL) correlated with non-esterified fatty acids (NEFA), and one crucial gene (CREBBP) influencing meat color. In conclusion, this investigation offers a new perspective on the differences in bovine muscle locations and contributes to the molecular understanding of bovine meat quality. Future research endeavors could delve deeper into the identified genes and pathways to enhance beef cattle’s quality and yield.

Reference | Related Articles | Metrics

Select

Linking atmospheric emission and deposition to accumulation of soil cadmium in the Middle-Lower Yangtze Plain, China

TANG Li-li, FU Bo-min, WU Yang, CAI Fu-chen, MA Yi-bing

2023, 22 (10): 3170-3181. DOI: 10.1016/j.jia.2023.05.016

Abstract （189） PDF in ScienceDirect

Cadmium (Cd) is one of the most toxic heavy metals in the environment. Atmospheric deposition has been found to be the main source of Cd pollution of soil on a large scale in China, and identification of the relationships between anthropogenic emission, atmospheric deposition, and Cd accumulation in soil is important for developing ways to mitigate Cd non-point pollution. In this study, the relationship between atmospheric emission, atmospheric deposition, and soil Cd accumulation in the Middle-Lower Yangtze Plain in China was investigated using datasets of atmospheric emission, deposition, and soil accumulation from the literatures published between 2000 and 2020. The results showed that the soil Cd accumulation rate in the study area exceeded the national average (4.0 μg kg^–1 yr^–1) and continued to accumulate in recent decades, although the average accumulation rate decreased from 9.45 μg kg^–1 yr^–1 (2000–2010 period) to 8.86 μg kg^–1 yr^–1 (2010–2020 period). The contribution of atmospheric deposition flux to Cd increment in the soil was in the range of 22–29%, with the atmospheric deposition flux decreasing from 0.54 mg m^–2 yr^–1 (2000–2010) to 0.48 mg m^–2 yr^–1 (2010–2020), both values being greater than the national average. Atmospheric Cd deposition and emission were highly correlated in a provincial administrative region, which is close to a ratio of 1.0. Emission factors may be in a state of dynamic change due to the influences of new Cd emission control technologies and environmental policies. As the main sources of Cd emissions, dust, and smoke emissions per ton of non-ferrous metal production decreased by 64.7% between the 2000–2010 and 2010–2020 periods. Although new environmental policies have been instigated, atmospheric emission of Cd is still excessive. It was hoped that the findings of this work would provide a scientific basis for the rational control of atmospheric emissions and Cd pollution of soil.

Reference | Related Articles | Metrics

Select

Moderate drought alleviate the damage of high temperature to grain quality by improving the starch synthesis of inferior grain in japonica rice

TONG Hui, DUAN Hua, WANG Sheng-jun, SU Jing-ping, SUN Yue, LIU Yan-qing, TANG Liang, LIU Xue-jun, CHEN Wen-fu

2022, 21 (10): 3094-3101. DOI: 10.1016/j.jia.2022.07.012

Abstract （208） PDF in ScienceDirect

In agricultural production, temperature and moisture are important factors affecting grain yield and quality. Although moderate drought at the grain-filling stage can effectively alleviate the damage caused by high temperature, the specific regulatory mechanism driving the effect of moderate drought at the high temperature on starch synthesis is still unclear. To explore the effects and mechanisms of high temperature and moderate drought on rice starch synthesis at the grain-filling stage, the activities of enzymes and expression levels of the genes involved in starch synthesis under four different treatments involving high temperature and/or water stress (CK, HT, WS, and HT+WS) were investigated in this study. The starch synthesis of a japonica inbred rice was measured under the four treatments during the grain filling. The results show that the effects of high temperature and moderate drought on grain filling mainly occur in the inferior grains of rice. Through the regulation of enzymes involved in starch synthesis and the expression levels of their main genes, the synthesis of rice starch can be affected. Therefore, the high temperature and moderate drought were antagonistic, and moderate drought can alleviate the damage to grain quality at a high temperature by improving the starch synthesis of inferior grains in japonica rice. This study provides a basis for stress-resistance cultivation and breeding strategies of rice with high temperature tolerance.

Reference | Related Articles | Metrics

Select

Yield performance and optimal nitrogen and phosphorus application rates in wheat and faba bean intercropping

XIAO Jing-xiu, ZHU Ying-an, BAI Wen-lian, LIU Zhen-yang, TANG Li, ZHENG Yi

2021, 20 (11): 3012-3025. DOI: 10.1016/S2095-3119(20)63489-X

Abstract （188） PDF in ScienceDirect

Yield performance in cereal and legume intercropping is related to nutrient management, however, the yield response of companion crops to nitrogen (N) input is inconclusive and only limited efforts have focused on rationed phosphorous (P) fertilization. In this study, two multi-year field experiments were implemented from 2014–2019 under identical conditions. Two factors in a randomized complete block design were adopted in both experiments. In field experiment 1, the two factors included three planting patterns (mono-cropped wheat (MW), mono-cropped faba bean (MF), and wheat and faba bean intercropping (W//F)) and four N application rates (N0, 0 kg N ha^–1; N1, 90 and 45 kg N ha^–1 for wheat and faba beans, respectively; N2, 180 and 90 kg N ha^–1 for wheat and faba beans, respectively; and N3, 270 and 135 kg N ha^–1 for wheat and faba beans, respectively). In field experiment 2, the two factors included three P application rates (P0, 0 kg P₂O₅ ha^–1; P1, 45 kg P₂O₅ha^–1; and P2, 90 kg P₂O₅ha^–1) and the same three planting patterns (MW, MF, and W//F). The yield performances of inter- and mono-cropped wheat and faba beans under different N and P application rates were analyzed and the optimal N and P rates for intercropped wheat (IW) and MW were estimated. The results revealed that intercropping favored wheat yield and was adverse to faba bean yield. Wheat yield increased by 18–26%, but faba bean yield decreased by 5–21% in W//F compared to MW and MF, respectively. The stimulated IW yield drove the yield advantage in W//F with an average land equivalent ratio (LER) of 1.12. N and P fertilization benefited IW yield, but reduced intercropped faba bean (IF) yield. Nevertheless, the partial LER of wheat (pLER_wheat) decreased with increasing N application rates, and the partial LER of faba bean (pLER_{faba bean}) decreased with increasing P application rates. Thus, LER decreased as N input increased and tended to decline as P rates increased. IW maintained a similar yield as MW, even under reduced 40–50% N fertilizer and 30–40% P fertilizer conditions. The estimated optimum N application rates for IW and MW were 150 and 168 kg ha^–1, respectively, and 63 and 62 kg ha^–1 for P₂O₅, respectively. In conclusion, W//F exhibited yield advantages due to stimulated IW yield, but the intercropping yield benefit decreased as N and P inputs increased. Thus, it was concluded that modulated N and P rates could maximize the economic and ecological functions of intercropping. Based on the results, rates of 150 kg N ha^–1 and 60 kg P₂O₅ha^–1 are recommended for IW production in southwestern China and places with similar conditions.

Reference | Related Articles | Metrics

Select

Quantitative design of yield components to simulate yield formation for maize in China

HOU Hai-peng, MA Wei, Mehmood Ali NOOR, TANG Li-yuan, LI Cong-feng, DING Zai-song, ZHAO Ming

2020, 19 (3): 668-679. DOI: 10.1016/S2095-3119(19)62661-4

Abstract （152） PDF in ScienceDirect

Maize (Zea mays L.) stands prominently as one of the major cereal crops in China as well as in the rest of the world. Therefore, predicting the growth and yield of maize for large areas through yield components under high-yielding environments will help in understanding the process of yield formation and yield potential under different environmental conditions. This accurate early assessment of yield requires accuracy in the formation process of yield components as well. In order to formulate the quantitative design for high yields of maize in China, yield performance parameters of quantitative design for high grain yields were evaluated in this study, by utilizing the yield performance equation with normalization of planting density. Planting density was evaluated by parameters including the maximum leaf area index and the maximum leaf area per plant. Results showed that the variation of the maximum leaf area per plant with varying plant density conformed to the Reciprocal Model, which proved to have excellent prediction with root mean square error (RMSE) value of 5.95%. Yield model estimation depicted that the best optimal maximum leaf area per plant was 0.63 times the potential maximum leaf area per plant of hybrids. Yield performance parameters for different yield levels were quantitatively designed based on the yield performance equation. Through validation of the yield performance model by simulating high yields of spring maize in the Inner Mongolia Autonomous Region and Jilin Province, China, and summer maize in Shandong Province, the yield performance equation showed excellent prediction with the satisfactory mean RMSE value (7.72%) of all the parameters. The present study provides theoretical support for the formulation of quantitative design for sustainable high yield of maize in China, through consideration of planting density normalization in the yield prediction process, providing there is no water and nutrient limitation.

Reference | Related Articles | Metrics

Select

Collision detection of virtual plant based on bounding volume hierarchy: A case study on virtual wheat

TANG Liang, SONG Wei-guo, HOU Tian-cheng, LIU Lei-lei, CAO Wei-xing, ZHU Yan

2018, 17 (2): 306-314. DOI: 10.1016/S2095-3119(17)61769-6

Abstract （802） PDF in ScienceDirect

Visualization of simulated crop growth and development is of significant interest to crop research and production. This study aims to address the phenomenon of organs cross-drawing by developing a method of collision detection for improving vivid 3D visualizations of virtual wheat crops. First, the triangular data of leaves are generated with the tessellation of non-uniform rational B-splines surfaces. Second, the bounding volumes (BVs) and bounding volume hierarchies (BVHs) of leaves are constructed based on the leaf morphological characteristics and the collision detection of two leaves are performed using the Separating Axis Theorem. Third, the detecting effect of the above method is compared with the methods of traditional BVHs, Axis-Aligned Bounding Box (AABB) tree, and Oriented Bounding Box (OBB) tree. Finally, the BVs of other organs (ear, stem, and leaf sheath) in virtual wheat plant are constructed based on their geometric morphology, and the collision detections are conducted at the organ, individual and population scales. The results indicate that the collision detection method developed in this study can accurately detect collisions between organs, especially at the plant canopy level with high collision frequency. This collision detection-based virtual crop visualization method could reduce the phenomenon of organs cross-drawing effectively and enhance the reality of visualizations.

Reference | Related Articles | Metrics

Select

Estimating the average treatment effect of adopting stress tolerant variety on rice yield in China

ZHOU Jie-hong, TANG Li-qun, Xiaohua Yu

2018, 17 (04): 940-948. DOI: 10.1016/S2095-3119(17)61848-3

Abstract （613） PDF （824KB）（450）

Climate extremes, characterized by droughts and floods, have become one of the major constraints to sustainable improvement of rice productivity. Variety choice, considered as one of the main adaptation measures, could help farmers reduce yield loss resulting from these extremes. Based on a three-year panel survey of 1 080 Chinese rice farms in major rice producing provinces, we assume Hicksian neutral technology and employ an IV regression to estimate the average treatment effect (ATE) on rice yield for adopting stress tolerant variety, and find that farmers who adopted the stress tolerant variety on average increased rice yield by 15.5% in comparison to the non-adopters.

Reference | Related Articles | Metrics

Select

Modeling curve dynamics and spatial geometry characteristics of rice leaves

ZHANG Yong-hui, TANG Liang, LIU Xiao-jun, LIU Lei-lei, CAO Wei-xing, ZHU Yan

2017, 16 (10): 2177-2190. DOI: 10.1016/S2095-3119(16)61597-6

Abstract （696） PDF in ScienceDirect

The objective of this work was to develop a dynamic model for describing leaf curves and a detailed spatial geometry model of the rice leaf (including sub-models for unexpanded leaf blades, expanded leaf blades, and leaf sheaths), and to realize three-dimensional (3D) dynamic visualization of rice leaves by combining relevant models. Based on the experimental data of different cultivars and nitrogen (N) rates, the time-course spatial data of leaf curves on the main stem were collected during the rice development stage, then a dynamic model of the rice leaf curve was developed using quantitative modeling technology. Further, a detailed 3D geometric model of rice leaves was built based on the spatial geometry technique and the non-uniform rational B-spline (NURBS) method. Validating the rice leaf curve model with independent field experiment data showed that the average distances between observed and predicted curves were less than 0.89 and 1.20 cm at the tilling and jointing stages, respectively. The proposed leaf curve model and leaf spatial geometry model together with the relevant previous models were used to simulate the spatial morphology and the color dynamics of a single leaf and of leaves on the rice plant after different growing days by 3D visualization technology. The validation of the leaf curve model and the results of leaf 3D visualization indicated that our leaf curve model and leaf spatial geometry model could efficiently predict the dynamics of rice leaf spatial morphology during leaf development stages. These results provide a technical support for related research on virtual rice.

Reference | Related Articles | Metrics

Select

Erect panicle super rice varieties enhance yield by harvest index advantages in high nitrogen and density conditions

TANG Liang, GAO Hong, Hirooka Yoshihiro, Homma Koki, Nakazaki Tetsuya, LIU Tian-sheng, Shiraiwa Tatsuhiko, XU Zheng-jin

2017, 16 (07): 1467-1473. DOI: 10.1016/S2095-3119(17)61667-8

Abstract （1294） PDF in ScienceDirect

The erect panicle (Ep) type is an important characteristic for japonica super rice in Northeast China and plays a significant role in enhancing yield. The Ep type is considered to be a genetic ideotype resource to the japonica super rice group by virtue of its agronomic advantages such as grain number per panicle and biomass. This study addresses the effects of nitrogen and planting density conditions on yielding performance regarding panicle type (PT) using the recombinant inbred line (RIL) population derived from the cross between an Ep variety Liaogeng 5 and non-Ep variety Wanlun 422. The genetics underlying the Ep type proved to be robust not only for panicle-type optimization but also plant height, panicle length, flag leaf length and seed density. We also found that regardless of nitrogen and density, correlation between harvest index (HI) and plant height was not significant in Ep type whatever the nitrogen and density. The application of Ep type provides a potential strategy for yield improvement by increasing biomass through HI maintainable in rice.

Reference | Related Articles | Metrics

Select

Discussion on strategy of grain quality improvement for super high yielding japonica rice in Northeast China

MAO Ting, LI Xu, JIANG Shu-kun, TANG Liang, WANG Jia-yu, XU Hai, XU Zheng-jin

2017, 16 (05): 1075-1083. DOI: 10.1016/S2095-3119(16)61563-0

Abstract （864） PDF in ScienceDirect

japonica rice is mainly distributed in Northeast China and accounts for 44.6% of the total cultivated area of japonica rice in China. The comprehensive using of inter-subspecies heterosis is the main breeding mode of super japonica rice varieties in this region. Improving rice quality at relative high yielding level is the current research focus. Performing crosses between indica and japonica lines allows for the recombination of regulatory genes and genetic backgrounds, leading to complicated genetic rice quality characteristics, which can be used to explore patterns of quality improvement. In the present study, we utilize recombinant inbred lines (RILs) derived from indica-japonica hybridization to analyze the effect factors of rice quality derived from genetic factors, which contain both regulatory genes concerning rice quality and genetic backgrounds’ random introduction frequency coming from indica (Di value), and the improvement strategy was further discussed. The regulatory genes involved in amylase content (Wx) and nitrogen utilization efficiency (NRT1.1B) were the major factors affecting the amylose content (AC) and protein content (PC) in RILs, respectively. Both the Di value and the major grain width gene (GS5) had regulatory effects on milled rice width (MRW) in RILs, and their interaction explained the major variance of MRW in the RILs. With the mediation of MRW and chalkiness degree (C), Di value had a further impact on head rice rate (HR), which was relatively poor when the Di value was over 40%. In Northeast China, the Di value should be lowered by backcrossing or multiple crosses during the breeding of indica-japonica hybridization to maintain the whole better HR and further to emphasize the use of favorable genes in individual selection.

Reference | Related Articles | Metrics

Select

Advances and prospects of super rice breeding in China

TANG Liang, XU Zheng-jin, CHEN Wen-fu

2017, 16 (05): 984-991. DOI: 10.1016/S2095-3119(16)61604-0

Abstract （1298） PDF in ScienceDirect

Super rice breeding in China has been very successful over the past 3 decades, and the Chinese government has made great efforts to support breeding and cultivation of both conventional and hybrid super rice. In this review, we focus on the progress in and potential of super rice breeding. After the establishment of the breeding theory and strategy of “generating an ideotype with strong heterosis through inter-subspecies hybridization, by using gene pyramiding to combine elite traits through composite-crossing to breed super rice varieties with both ideotype and strong hybrid vigor”, a series of major breakthroughs have been achieved in both conventional and super hybrid rice breeding. A number of new genetic materials with ideotype have been created successfully, and the Ministry of Agriculture of China has approved 156 novel super rice varieties and combinations for commercialization. During the Developing the Super Rice Varieties Program, great attention has also been paid to the integration and demonstration of the rice production technology. Collaboration between industry and university researchers has led to technological innovations and initiation of a demonstration system for super hybrid rice. With widespread cultivation of super rice with higher quality and yield, as well as resistance or tolerance to abiotic or biotic stresses, the yield of rice production per unit has reached a new level. In addition to increased quality and yield, hybrid rice breeding has also led to improvements in many other agronomic traits, such as resistance to pests and diseases, resistance to lodging, and optimized light distribution in population. Achievements in super rice breeding and innovation in rice production have made major contributions to the progress in rice sciences and worldwide food security.

Reference | Related Articles | Metrics

Select

20 years’ development of super rice in China- The 20th anniversary of the super rice in China

CHEN Wen-fu, XU Zheng-jin, TANG Liang

2017, 16 (05): 981-983. DOI: 10.1016/S2095-3119(16)61612-X

Abstract （1061） PDF in ScienceDirect

Reference | Related Articles | Metrics

Select

Quantifying the spatial variation in the potential productivity and yield gap of winter wheat in China

ZHANG Shi-yuan, ZHANG Xiao-hu, QIU Xiao-lei, TANG Liang, ZHU Yan, CAO Wei-xing, LIU Lei-lei

2017, 16 (04): 845-857. DOI: 10.1016/S2095-3119(16)61467-3

Abstract （957） PDF in ScienceDirect

Despite the improvement in cultivar characters and management practices, large gaps between the attainable and potential yields still exist in winter wheat of China. Quantifying the crop potential yield is essential for estimating the food production capacity and improving agricultural policies to ensure food security. Gradually descending models and geographic information system (GIS) technology were employed to characterize the spatial variability of potential yields and yield gaps in winter wheat across the main production region of China. The results showed that during 2000–2010, the average potential yield limited by thermal resource (YG_T) was 23.2 Mg ha^–1, with larger value in the northern area relative to the southern area. The potential yield limited by the water supply (YG_W) generally decreased from north to south, with an average value of 1.9 Mg ha^–1 across the entire study region. The highest YG_W in the north sub-region (NS) implied that the irrigation and drainage conditions in this sub-region must be improved. The averaged yield loss of winter wheat from nutrient deficiency (YG_N) varied between 2.1 and 3.1 Mg ha^–1 in the study area, which was greater than the yield loss caused by water limitation. The potential decrease in yield from photo-thermal-water-nutrient-limited production to actual yield (YG_O) was over 6.0 Mg ha^–1, ranging from 4.9 to 8.3 Mg ha^–1 across the entire study region, and it was more obvious in the southern area than in the northern area. These findings suggest that across the main winter wheat production region, the highest yield gap was induced by thermal resources, followed by other factors, such as the level of farming technology, social policy and economic feasibility. Furthermore, there are opportunities to narrow the yield gaps by making full use of climatic resources and developing a reasonable production plan for winter wheat crops. Thus, meeting the challenges of food security and sustainability in the coming decades is possible but will require considerable changes in water and nutrient management and socio-economic policies.

Reference | Related Articles | Metrics

Select

Cow manure and cow manure-derived biochar application as a soil amendment for reducing cadmium availability and accumulation by Brassica chinensis L. in acidic red soil

Yasmin Khan Kiran, Ali Barkat, CUI Xiao-qiang, FENG Ying, PAN Feng-shan, TANG Lin, YANG Xiao-e

2017, 16 (03): 725-734. DOI: 10.1016/S2095-3119(16)61488-0

Abstract （1258） PDF in ScienceDirect

Organic amendment is a promising, in situ phytostabilization approach to alleviate the phytotoxic effects of heavy metal contaminated soils. The aim of this study was to evaluate the feasibility of cow manure (CM) and its derived biochar (CMB) as a soil amendment on cadmium (Cd) availability and accumulation in low and high Cd-accumulating cultivars of Brassica chinensis L. grown in an acidic red soil. CM and CMB were applied to Cd-contaminated acidic red soil at the rates of 0, 3.0 and 6.0% (w/w). Application of CMB was significantly more effective than that of CM, as it reduced the availability of Cd in soil by 34.3–69.9% and its bioaccumulation in the low Cd accumulator, Aijiaoheiye 333, by 51.2 and 67.4%, respectively. The addition of CMB significantly increased the extractability and accumulation of trace metals (Zn, Mn, Fe, and Cu) by plants and improved plant biomass production. CMB application, combined with utilizing low Cd accumulating cultivars represents a new, sustainable strategy to alleviate the toxic effects on Cd and improve food safety.

Reference | Related Articles | Metrics

Select

Experimental and genomic evidence for the indica-type cytoplasmic effect in Oryza sativa L. ssp. japonica

LIU You-hong, TANG Liang, XU Quan, MA Dian-rong, ZHAO Ming-hui, SUN Jian, CHEN Wen-fu

2016, 15 (10): 2183-2191. DOI: 10.1016/S2095-3119(15)61190-X

Abstract （1501） PDF in ScienceDirect

Cytoplasmic effects are important agronomical phenomena that have generated widespread interest in both theory and application. In the present study, five high yield rice cultivars (Oryza sativa L. ssp. japonica) in large-scale cultivation in northeast China were determined to possess Oryza sativa L. ssp. indica-type cytoplasm using cytoplasmic subspecies-specific molecular markers. This was confirmed by cytoplasmic genome-wide single nucleotide polymorphisms (SNPs) and functional gene sequencing. Two of these five japonica cultivars were core breeding parents with high yield and the other three were super-high-yield varieties registered by the Ministry of Agriculture of China. We constructed nuclear substitution lines to further demonstrate whether and how this indica-type cytoplasm contributed to yield improvement by comparing yield components. The results showed that under the same japonica nuclear background, the lines with indica-type cytoplasm had a significant decrease in tillers in exchange for increased grain number per panicle compared with their recurrent parents. Our results implied that botanical basis of this cytoplasmic effect was to reduce the plant’s branching differentiation to produce more floral organs under the constant nutrition. Our findings open another door for the utilization of inter-subspecific hybridization for the improvement of rice cultivar.

Reference | Related Articles | Metrics

Select

Development of a multiplex reverse transcription-PCR assay for simultaneous detection of garlic viruses

HU Xin-xi, LEI Yan, WANG Pei, TANG Lin-fei, HE Chang-zheng, SONG Yong, XIONG Xing-yao, NIE Xian-zhou

2015, 14 (5): 900-908. DOI: 10.1016/S2095-3119(14)60892-3

Abstract （2269） PDF in ScienceDirect

A preliminary screening for garlic viruses in garlic plants in Hunan, China, using existing monoplex (simplex) reverse transcription- polymerase chain reaction (RT-PCR) procedures detected four viruses/virus groups. These viruses/virus groups were Onion yellow dwarf virus (OYDV), Leek yellow stripe virus (LYSV), Shallot latent virus (SLV) and allexiviruses (e.g., garlic viruses A, B, C, D, E, X). Sequence analysis of the projected allexivirus amplicons revealed the allexivirus in the infected garlic plants was Garlic virus D (GarV-D), which shared 92–97% sequence identities with various isolates from the world. A multiplex RT-PCR (mRT-PCR) was therefore developed to simultaneously detect and differentiate the four viruses/virus groups. To achieve this, four primer pairs targeting allexiviruses, OYDV, LYSV and SLV were designed. The anticipated amplicon sizes are 183 bp (allexiviruses), 265 bp (OYDV), 404 bp (LYSV) and 592 bp (SLV), respectively. All primer pairs produced virus-specific fragments in both simplex and multiplex formats, thus confirming the efficacy of the newly developed mRT-PCR for detection of these viruses. The mRT-PCR further was evaluated by applying it to garlic plant samples collected in two geographic locations in Hunan. Allexiviruses, OYDV, LYSV and SLV were detected in 50.9, 40.3, 28.3 and 58.5% of leaf samples, respectively; and mixed infections with two or more viruses accounted for 54% of the garlic samples. The results obtained by mRT-PCR were confirmed by simplex RT-PCR assays. In conclusion, this newly developed mRT-PCR provides a rapid, sensitive and reliable method for the detection and identification of major garlic viruses.

Reference | Related Articles | Metrics

Select

Modeling Dynamics of Leaf Color Based on RGB Value in Rice

ZHANG Yong-hui, TANG Liang, LIU Xiao-jun, LIU Lei-lei, CAO Wei-xing , ZHU Yan

2014, 13 (4): 749-759. DOI: 10.1016/S2095-3119(13)60391-3

Abstract （2287） PDF in ScienceDirect

This paper was to develop a model for simulating the leaf color changes in rice (Oryza sativa L.) based on RGB (red, green, and blue) values. Based on rice experiment data with different cultivars and nitrogen (N) rates, the time-course RGB values of each leaf on main stem were collected during the growth period in rice, and a model for simulating the dynamics of leaf color in rice was then developed using quantitative modeling technology. The results showed that the RGB values of leaf color gradually decreased from the initial values (light green) to the steady values (green) during the first stage, remained the steady values (green) during the second stage, then gradually increased to the final values (from green to yellow) during the third stage. The decreasing linear functions, constant functions and increasing linear functions were used to simulate the changes in RGB values of leaf color at the first, second and third stages with growing degree days (GDD), respectively; two cultivar parameters, MatRGB (leaf color matrix) and AR (a vector composed of the ratio of the cumulative GDD of each stage during color change process of leaf n to that during leaf n drawn under adequate N status), were introduced to quantify the genetic characters in RGB values of leaf color and in durations of different stages during leaf color change, respectively; FN (N impact factor) was used to quantify the effects of N levels on RGB values of leaf color and on durations of different stages during leaf color change; linear functions were applied to simulate the changes in leaf color along the leaf midvein direction during leaf development process. Validation of the models with the independent experiment dataset exhibited that the root mean square errors (RMSE) between the observed and simulated RGB values were among 8 to 13, the relative RMSE (RRMSE) were among 8 to 10%, the mean absolute differences (da) were among 3.85 to 6.90, and the ratio of da to the mean observation values (dap) were among 3.04 to 4.90%. In addition, the leaf color model was used to render the leaf color change over growth progress using the technology of visualization, with a good performance on predicting dynamic changes in rice leaf color. These results would provide a technical support for further developing virtual plant during rice growth and development.

Reference | Related Articles | Metrics

Select

Spatial and Temporal Characteristics of Rice Potential Productivity and Potential Yield Increment in Main Production Regions of China

JIANG Xiao-jian, TANG Liang, LIU Xiao-jun, CAO Wei-xing , ZHU Yan

2013, 12 (1): 45-56. DOI: 10.1016/S2095-3119(13)60204-X

Abstract （1762） PDF in ScienceDirect

The vast area and marked variation of China make it difficult to predict the impact of climate changes on rice productivity in different regions. Therefore, analyzing the spatial and temporal characteristics of rice potential productivity and predicting the possible yield increment in main rice production regions of China is important for guiding rice production and ensuring food security. Using meteorological data of main rice production regions from 1961 to 1970 (the 1960s) and from 1996 to 2005 (the 2000s) provided by 333 stations, the potential photosynthetic, photo-thermal and climatic productivities in rice crop of the 1960s and 2000s in main rice production regions of China were predicted, and differences in the spatial and temporal distribution characteristics between two decades were analyzed. Additionally, the potential yield increment based on the high yield target and actual yield of rice in the 2000s were predicted. Compared with the 1960s, the potential photosynthetic productivity of the 2000s was seen to have decreased by 5.40%, with rates in northeastern and southwestern China found to be lower than those in central and southern China. The potential photo-thermal productivity was generally seen to decrease (2.56%) throughout main rice production regions, decreasing most in central and southern China. However, an increase was seen in northeastern and southwestern China. The potential climatic productivity was observed to be lower (7.44%) in the 2000s compared to the 1960s, but increased in parts of central and southern China. The potential yield increment from the actual yield to high yield target in the 2000s were no more than 6×103 kg ha-1 and ranged from 6×103 to 12×103 kg ha-1 in most of the single- and double-cropping rice growing regions, respectively. The yield increasing potential from the high yield target to the potential photo-thermal productivity in 2000s were less than 10×103 kg ha-1 and ranged from 10×103 to 30×103 kg ha-1 in most of the single- and double-cropping rice growing regions, respectively. The potential yield increment contributed by irrigation was between 5×103 and 20×103 kg ha-1, and between 20×103 and 40×103 kg ha-1 in most of the single- and double-cropping rice growing regions, respectively. These findings suggested that the high yield could be optimized by making full use of climatic resources and through a reasonable management plan in rice crop.

Reference | Related Articles | Metrics

About JIA

Editorial board

For authors