探究影响牛肉品质的遗传因素和代谢物分子对提高牛肉品质和满足消费者需求至关重要。肉牛不同部位的肉质特点差异很大，价格也有所不同。因此，本研究旨在评价秦川牛四个不同部位（里脊、外脊、上脑和眼肌）的10个肉质性状，包括总蛋白含量（TPC）、肌内脂肪含量（IMF）、游离脂肪酸 (NEFA)、肉色（L*、a* 和 b*）、剪切力 (SF)、蒸煮损失 (CL)、屠宰后0小时pH（pH0）和屠宰后24小时pH（pH24）。进一步进行转录组和代谢组测序分析，采用加权共表达网络分析（WGCNA）方法探索与性状相关的基因和代谢物模块，构建蛋白-蛋白互作网络（PPI），筛选关键基因和代谢物，以及共同富集的KEGG通路。我们筛选到了3个与肌内脂肪含量（IMF）相关的关键基因（NDUFAB1、NDUFA12和NDUFB7），3个与游离脂肪酸（NEFA）相关的关键基因（CSRP3、ACAA3和ACADVL），1个与肉色相关的关键基因（CREBBP）。本研究为揭示牛不同肌肉部位的差异提供了新的视角，下一步基于本研究筛选到的基因和通路开展深入研究，将有助于改善牛肉品质。

温度和水分是影响水稻产量和品质形成的重要因子，灌浆结实期适度的干旱能够有效的缓解高温胁迫对水稻造成的伤害，但有关其淀粉合成的调控机理尚不清楚。为探明灌浆结实期高温与干旱对水稻淀粉合成的影响及其生理机制，本试验研究了4个不同处理下（对照（CK）、高温（HT）、适度干旱（WS）、高温干旱（HT+WS））常规粳稻淀粉相关酶活性及其基因的表达水平。结果表明高温和干旱对籽粒灌浆的影响主要发生在弱势粒中，并通过调节参与淀粉合成相关酶活性及其主效基因的表达水平，进而影响稻米淀粉的合成。高温和干旱有拮抗作用，适度干旱能够改善高温对稻米品质的影响。

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.

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.

   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.

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.

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.

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.

    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.

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.

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.