• Five QTLs associated with weeping traits on chromosome 7 were identified by BSR-seq.

Weeping species are used both as ornamental plants and for breeding dwarf plant types. However, exploration of casual genes controlling weeping traits is rather limited. Here, we identified individuals with contrasting phenotypes from an F₁ bi-parental mapping population of Prunus mume which was developed from a cross between the upright cultivar ‘Liuban’ and the weeping cultivar ‘Fentai Chuizhi’. Bulked segregant RNA sequencing was used and five QTLs on Chromosome 7 were identified. The Pm024074 (PmUGT72B3) allele, belonging to the UDP-glycosyltransferase superfamily containing the coniferyl-alcohol glucosyltransferase domain, was identified in a genomic region overlapping with a previously identified QTL, and had a synonymous transition of T⁶⁶ (upright) to C (weeping) in the coding sequence and a 470-bp deletion in the promoter region. Pm024074 had exceptionally high expression in buds and stems of weeping P. mume. Weighted correlation network analysis indicates that genes neighboring Pm024074 were significantly associated with plant architecture. In addition, a reliable single nucleotide polymorphism marker was developed based on the variation in the Pm024074 gene, providing precise marker-assisted breeding for weeping traits. This study provides insights into the genetic mechanism governing the weeping trait in P. mume, and indicates potential applications for the manipulation of tree architecture.

• Metabolites of fresh tea shoots at harvest were profiled.

Metabolites, especially secondary metabolites, are very important in the adaption of tea plants and the quality of tea products. Here, we focus on the seasonal variation in metabolites of fresh tea shoots and their regulatory mechanism at the transcriptional level. The metabolic profiles of fresh tea shoots of 10 tea accessions collected in spring, summer, and autumn were analyzed using ultra-performance liquid chromatography coupled with quadrupole-obitrap mass spectrometry. We focused on the metabolites and key genes in the phenylpropanoid/flavonoid pathway integrated with transcriptome analysis. Multivariate statistical analysis indicates that metabolites were distinctly different with seasonal alternation. Flavonoids, amino acids, organic acids and alkaloids were the predominant metabolites. Levels of most key genes and downstream compounds in the flavonoid pathway were lowest in spring but the catechin quality index was highest in spring. The regulatory pathway was explored by constructing a metabolite correlation network and a weighted gene co-expression network.

• The contents of anthocyanin and AsA in red-flesh apples are higher than that in non-red-flesh apples.

Ascorbic acid (AsA, vitamin C) is involved in the regulation of many aspects of plant growth and development. It is an essential micronutrient for humans and can prevent scurvy, maintain the health of gums and blood vessels, reduce the level of plasma cholesterol and enhance the immune systen. Apple cultivars Orin and Guanghui were crossed to obtain a group of hybrid offspring with and without red flesh in the course of assessing apple germplasm resources. Unexpectedly, the red-flesh apples had higher AsA contents than other apples. Further studies showed that the anthocyanin biosynthetic regulator MdMYB1 directly activates the expression of dehydroascorbate reductase gene MdDHAR, thus promoting the activity of the DHAR enzyme and the accumulation of AsA. This finding reveals the mechanism leading to high AsA levels in red-flesh apples and suggests a new idea to cultivate red-flesh apples with high AsA contents and produce AsA efficiently and without pollution.

• A LEA family gene (PtrLEA7)was cloned from Poncirus trifoliata.

Late embryogenesis abundant (LEA) genes encode highly hydrophilic proteins that are essential in abiotic stress responses. However, most LEA genes in higher plants have not yet been investigated. This study identified an LEA family gene (PtrLEA7) from Poncirus trifoliata and studied its function in drought tolerance. The full-length coding sequence of PtrLEA7 was 420 bp encoding a protein of 139 amino acids. Phylogenetic analysis shows that PtrLEA7 protein belongs to the LEA_4 subfamily. Expression profiling by qPCR found that PtrLEA7 was strongly induced by dehydration, cold and ABA treatments, and slightly induced by salt stress. Subcellular localization reveals that PtrLEA7 protein was located in both cytoplasm and nucleus. To investigate its function, transgenic plants of both tobacco and Poncirus trifoliata overexpressing PtrLEA7 were obtained. Stress tolerance assays show that overexpression lines had enhanced dehydration and drought tolerance compared with wild type plants, indicating that PtrLEA7 positively regulates drought tolerance. In addition, transgenic plants had much higher expression levels of three antioxidant enzyme genes (CAT, SOD and POD) and significantly increased catalase enzyme activity, accompanied by reduced reactive oxygen species accumulation in comparison with wild type plants. Collectively, this study demonstrates that PtrLEA7 can confer enhanced drought tolerance partially via enhancing antioxidant capacity.

•MdSIZ1 RNAi transgenic apple trees are drought tolerance than wild type—GL-3.

Drought stress typically causes heavy losses in apple production and uncovering the mechanisms by which apple tolerates drought stress is important in apple breeding. MdSIZ1 is a SUMO (small ubiquitin-like modifier) E3 ligase that promotes SUMO binding to substrate proteins. Here, we demonstrate that MdSIZ1 in apple has a negative relationship with drought tolerance. MdSIZ1 RNAi transgenic apple trees had a higher survival rate after drought stress. During drought stress they had higher leaf water potential, reduced ion leakage, lower H₂O₂ and malondialdehyde contents, and higher catalase activity. In addition, MdSIZ1 RNAi transgenic plants had a higher net photosynthetic rate during the latter period of drought stress. Finally, the transgenic apple trees also altered expression levels of some microRNAs in response to drought stress. Taken together, these results indicate that apple MdSIZ1 negatively regulates drought stress by enhancing leaf water-holding capacity and antioxidant enzyme activity.

• ICLS combines the benefits of specialization with increased resilience of the system.

Ongoing specialization of crop and livestock systems provides socioeconomic benefits to the farmer but has led to greater externalization of environmental costs when compared to mixed farming systems. Better integration of crop and livestock systems offers great potential to rebalance the economic and environmental trade-offs in both systems. The aims of this study were to analyze changes in farm structure and review and evaluate the potential for reintegrating specialized intensive crop and livestock systems, with specific emphasis on identifying the co-benefits and barriers to reintegration. Historically, animals were essential to recycle nutrients in the farming system but this became less important with the availability of synthetic fertilisers. Although mixed farm systems can be economically attractive, benefits of scale combined with socio-economic factors have resulted in on-farm and regional specialization with negative environmental impacts. Reintegration is therefore needed to reduce nutrient surpluses at farm, regional and national levels, and to improve soil quality in intensive cropping systems. Reintegration offers practical and cost-effective options to widen crop rotations and promotes the use of organic inputs and associated benefits, reducing dependency on synthetic fertilisers, biocides and manure processing costs. Circular agriculture goes beyond manure management and requires adaptation of both food production and consumption patterns, matching local capacity to produce with food demand. Consequently, feed transport, greenhouse gas emissions, nutrient surpluses and nutrient losses to the environment can be reduced. It is concluded that reintegration of specialized farms within a region can provide benefits to farmers but may also lead to further intensification of land use. New approaches within a food system context offer alternatives for reintegration, but require strong policy incentives which show clear, tangible and lasting benefits for farmers, the environment and the wider community.

• China is now the largest egg production country worldwide

Eggs are one of the most nutritious and affordable animal products worldwide. From 1985, egg production in China has retained the leading place in the world. A total of 33 Mt of eggs were produced in 2019 representing ˃ 40% of the world total production. Egg production in China is characterized by diversity in several aspects, including layer breeds, products and production systems. New breeds and synthetic lines are developed to improve the genetic potentials of egg production and feed efficiency of layers. In the past, layer farms were run mostly by small households with 100 to 1000 layers per farm. Over the past decades, egg production in China has developed toward standardization and expansion of production systems, and many of these modern intensive farms raise millions of layers. Although the Chinese egg products maintain strong competitiveness over other animal products and imported egg products, the egg industry will grow at a slower pace compared to the past. Chinese consumers are more concerned about the quality and safety of eggs and egg products, as well as the environmental issues related to animal production, which presents challenges for the Chinese egg industry.

•Large-scale industrial pork production enterprises are preferred in China in the future.

This paper reviews the changes in pork production in China, the largest pork producing and consuming nation in the world. The pork sector in China has changed dramatically since the 1990s, with large-scale intensive pork production systems replacing the former, exclusively family-based pork production systems. Modern breeding, feeding, vaccinating, and management technologies are widely used now. However, smallholders still account for a large proportion of the total production. The intensification and specialization of the pork sector is expected to continue in the future, but there is increasing awareness and pressure to develop more environmentally-sustainable production systems. The relative shortage of domestically produced feed, the low utilization efficiency of feed ingredients, the large emissions of nitrogen and phosphorus to the environment, the high use of antibiotics, and the presence of residual metals in manures are very large challenges for the pork sector nowadays. To solve these problems, techniques including new feed resource utilization, precise feeding, low-protein diets, alternatives to antibiotics and increased manure recycling are all important topics and research directions today. With new techniques and management approaches, it is possible to build more sustainable pork production systems in China.

• NZ dairy farming systems are based on year-round grazing of perennial pasture (ryegrass/white clover).

This paper provides an overview of the range of dairy pasture grazing systems used in New Zealand (NZ), the changes with increased inputs over time and associated key environmental effects including nitrogen (N) leaching and greenhouse gas (GHG) emissions. NZ dairy farming systems are based on year-round grazing and seasonal milk production on perennial ryegrass/clover pasture where cows are rotationally grazed in paddocks. There was an increase in stocking rate on NZ dairy farms from 2.62 cows ha⁻¹ in 2000/2001 to 2.84 cows ha⁻¹ in 2015/2016. During the same period annual milk solids production increased from 315 to 378 kg·yr⁻¹ per cow. This performance has coincided with an increase in N fertilizer use (by ~ 30%) and a twofold increase in externally-sourced feeds. Externally-sourced feeds with a low protein concentration (e.g., maize silage) can increase the efficiency of N utilization and potentially reduce N losses per unit of production. Off-paddock facilities (such as standoff or feed pads) are often used to restrict grazing during very wet winter conditions. A systems analysis of contrasting dairy farms in Waikato (largest NZ dairying region) indicates that the increased input would result in an increase in per-cow milk production but little change in efficiency of milk production from a total land use perspective. This analysis also shows that the increased inputs caused an 11% decrease in N footprint (i.e., N emissions per unit of milk production) and a 2% increase in C footprint (i.e., greenhouse gas (GHG) emissions per unit of milk production).

• Current intensification trends in the Rio de la Plata need urgent re-direction.

The Rio de la Plata region comprises central Argentina, Uruguay, and southern Brazil. Modern agriculture developed around 1900 with recent decades being characterized by the advance of cropping areas over native grasslands. Highly specialized agriculture has decoupled crop and livestock production but has succeeded in intensifying yields. However, significant losses of ecosystem services have been reported. Thus, questions have been raised on the sustainability of this pathway. A glance at world regions that have experienced similar trends suggests that an urgent course correction is needed. A major concern has been the lack of diversity in regions with highly specialized agriculture, promoting renewed interest in integrated crop-livestock systems (ICLS), not only because ICLS are more diverse than specialized systems, but also because they are rare examples of reconciliation between agroecosystem intensification and environmental quality. Consequently, this paper discusses alternatives to redesign multifunctional landscapes based on ICLS. Recent data provide evidence that recoupling crop and animal production increases the resilience of nutrient cycling functions and economic indicators to external stressors, enabling these systems to face climate-market uncertainty and reconcile food production with the provision of diverse ecosystem services. Finally, these concepts are exemplified in case studies where this perspective has been successfully applied.

• Manure utilization is hindered by separate specialist crop and livestock production systems.

Livestock numbers in China have more than tripled between 1980 and 2017. The increase in the number of intensive livestock production systems has created the challenges of decoupled crop and livestock systems, low utilization of manures in croplands, and subsequent environmental pollution. Correspondingly, the government has enacted a series of policies and regulations to increase the sustainability of livestock production. This paper reviews the objectives of these policies and regulations and their impacts on manure management. Since 2017 there have been two policy guides to speed up the appropriate use of manures, three action plans for increasing manure recycling, and one technical guide to calculate nutrient balances. Requirements of manure pollution control and recycling for improved environmental performance of livestock production systems were included in three revised environmental laws. Most recent survey data indicate that the utilization of livestock manures was 70% in 2017, including that used as fertilizer and/or for production of energy. The targets for manure utilization are 75% in 2020 and 90% in 2035. To achieve these targets and promote ‘green livestock production’, additional changes are needed including the use of third-party enterprises that facilitate manure exchange between farms and a more integrated manure nutrient management approach.

• Livestock manure was the main organic waste in urban and peri-urban areas.

Urban population growth is driving the expansion of urban and peri-urban agriculture (UPA) in developing countries. UPA is providing nutritious food to residents but the manures produced by UPA livestock farms and other wastes are not properly recycled. This paper explores the effects of four scenarios: (1) a reference scenario (business as usual), (2) increased urbanization, (3) UPA intensification, and (4) improved technology, on food-protein self-sufficiency, manure nitrogen (N) recycling and balances for four different zones in a small city (Jimma) in Ethiopia during the period 2015-2050. An N mass flow model with data from farm surveys, field experiments and literature was used. A field experiment was conducted and N use efficiency and N fertilizer replacement values differed among the five types of composts derived from urban livestock manures and kitchen wastes. The N use efficiency and N fertilizer replacement values were used in the N mass flow model.

Livestock manures were the main organic wastes in urban areas, although only 20 to 40% of animal-sourced food consumed was produced in UPA, and only 14 to 19% of protein intake by residents was animal-based. Scenarios indicate that manure production in UPA will increase 3 to 10 times between 2015 and 2050, depending on urbanization and UPA intensification. Only 13 to 38% of manure N will be recycled in croplands. Farm-gate N balances of UPA livestock farms will increase to>1 t·ha⁻¹ in 2050. Doubling livestock productivity and feed protein conversion to animal-sourced food will roughly halve manure N production.

Costs of waste recycling were high and indicate the need for government incentives. Results of these senarios are wake-up calls for all stakeholders and indicate alternative pathways.

• Degree of integration of crop and livestock was insufficient on mixed smallholdings.

The proportion of industrial livestock in China has increased over the past 30 years, which increases animal performance but causes the decoupling of crop and livestock production. Here, we aimed to quantify nutrient flows, nutrient use efficiency, and nutrient losses in different livestock systems in the North China Plain based on the NUFER-farm model. Activity data were collected by face-to-face surveys on pig and dairy (41 livestock farms) during 2016–2018. The two systems included industrial farms and mixed smallholdings. In mixed smallholdings, 4.0% and 9.6% of pig and dairy feed dry matter (DM) were derived from household farmland, but 4.8% and 9.3% of manure DM recycled to household farmland. Nutrient use efficiency in industrial farms was higher than in mixed smallholdings at animal level, herd level, and system level. To produce 1 kg N and P in animal products, nutrient losses in industrial pig farms (2.0 kg N and 1.3 kg P) were lower than in mixed pig smallholdings, nutrient losses in industrial dairy farms (2.7 kg N and 2.2 kg P) were slightly higher than in mixed dairy smallholdings. Liquid manure discharge in industrial farms was the main losses pathway in contrast to mixed smallholdings. This study suggests that feed localization can reduce nutrient surpluses at the district level. It is necessary to improve manure management and increase the degree of integrated crop-livestock in smallholdings. In industrial farms, it is desirable to increase the liquid manure recycling ratio through cooperating livestock and crop production at the district level.

• Monitoring data of>5000 dairy farms collected and examined in uniform manner.

Many grassland-based dairy farms are intensifying production, i.e., produce more milk per ha of land in response to the increasing demand for milk (by about 2% per year) in a globalized market. However, intensive dairy farming has been implicated for its resources use, ammonia and greenhouse gas emissions, and eutrophication impacts. This paper addresses the question of how the intensity of dairy production relates to N and P surpluses and use efficiencies on farms subjected to agri-environmental regulations. Detailed monitoring data were analyzed from 2858 grassland-based dairy farms in The Netherlands for the year 2015. The farms produced on average 925 Mg·yr⁻¹ milk. Milk production per ha ranged from<10 to>30 Mg·ha⁻¹·yr⁻¹. Purchased feed and manure export strongly increased with the level of intensification. Surpluses of N and P at farm level remained constant and ammonia emissions per kg milk decreased with the level of intensification. In conclusion, N and P surpluses did not differ much among dairy farms greatly differing in intensity due to legal N and P application limits and obligatory export of manure surpluses to other farms. Further, N and P use efficiencies also did not differ among dairy farms differing in intensity provided the externalization of feed production was accounted for. This paper provides lessons for proper monitoring and control of N and P cycling in dairy farming.

• Grassland-based livestock production systems cover large areas in China.

Interactions between crops and livestock have been at the core of the evolution of many agricultural systems. In this paper, we review the development and characteristics of mixed crop-livestock systems, with a focus on grassland-based systems, as these cover large areas in China, and face several challenges. Following the transition from the original hunting and foraging systems to a sedentary lifestyle with integrated crop-livestock production systems some 8000 years ago, a range of different mixed systems have developed, depending on rainfall, solar radiation and temperature, culture and markets. We describe 5 main types of integrated systems, (1) livestock and rangeland, (2) livestock and grain production, (3) livestock and crop – grassland rotations, (4) livestock, crops and forest (silvo-pasture), and (5) livestock, crops and fish ponds. Next, two of these mixed systems are described in greater detail, i.e., the mountain-oasis-desert system and its modifications in arid and semi-arid regions, and the integrated crop-livestock production systems on the Loess Plateau. In general, crop-livestock interactions in integrated systems have significant positive effects on crop production, livestock production, energy use efficiency and economic profitability. We conclude that improved integration of crop-livestock production systems is one of the most important ways for achieving a more sustainable development of animal agriculture in China.

• Intercropping is a useful practice when agricultural sustainability is emphasized.

Intercropping is a traditional farming system that increases crop diversity to strengthen agroecosystem functions while decreasing chemical inputs and minimizing negative environmental effects of crop production. Intercropping is currently considerable interest because of its importance in sustainable agriculture. Here, we synthesize the factors that make intercropping a sustainable means of food production by integrating biodiversity of natural ecosystems and crop diversity. In addition to well-known yield increases, intercropping can also increase yield stability over the long term and increase systemic resistance to plant diseases, pests and other unfavorable factors (e.g. nutrient deficiencies). The efficient use of resources can save mineral fertilizer inputs, reduce environmental pollution risks and greenhouse gas emissions caused by agriculture, thus mitigating global climate change. Intercropping potentially increases above- and below-ground biodiversity of various taxa at field scale, consequently it enhances ecosystem services. Complementarity and selection effects allow a better understanding the mechanisms behind enhanced ecosystem functioning. The development of mechanization is essential for large-scale application of intercropping. Agroecosystem multifunctionality and soil health should be priority topics in future research on intercropping.

• AGD aims for a green environment, sustainable agriculture and clean water.

Crop and livestock production are essential to maintain food security. In China, crop and livestock production were integrated in the past. Today, small backyard systems are still integrated but the larger livestock farms are landless and largely geographically separated from crop production systems. As a result, there is less recycling of animal manures and there are lower nutrient use efficiencies in the Chinese food production systems. This, in turn, results in considerable losses of nutrients, causing water pollution and harmful algal blooms in Chinese lakes, rivers and seas. To turn the tide, there is a need for agricultural “green” development for food production through reintegrating crop and livestock production. An additional wish is to turn the Chinese water systems “blue” to secure clean water for current and future generations. In this paper, current knowledge is summarized to identify promising interventions for reintegrating crop and livestock production toward clean water. Technical, social, economic, policy and environmental interventions are addressed and examples are given. The paper highlights recommended next steps to achieve “green” agriculture and “blue” water in China.

• Livestock production in North America has moved to fewer farms with greater inventories

Livestock production in the United States (US) and Canada is diverse, but shows a common trend in most livestock sectors toward fewer farms producing the majority of animal products despite a large number of farms still small in production scale. The migration to larger and more concentrated animal feeding operations in beef finishing and poultry, swine, and dairy production allows processors to streamline supplies to meet market demand for abundant, low-cost livestock products, whether that be for packaged meat, dairy products, or eggs. With concentration of livestock operations comes the challenge of managing manures. When sufficient land is available and nutrients are needed, livestock manure is an excellent nutrient source and land application is the preferred method of recycling this resource. However, when livestock production is constrained in a geographical area and animal densities are high, manure may become an environmental liability with potentially greater risk for runoff and leaching of nutrients, emission of odors, ammonia, and greenhouse gases, and release to the environment of pathogens and chemicals of emerging concern. Addressing these challenges now and into the future requires learning from mistakes and adopting successful approaches. We describe different levels of integration between livestock and crop producers in New York, British Columbia, and the south-eastern US as learning opportunities to improve economic and environmental sustainability. Examples show that effective solutions should recognize (1) manure has value and is not just a cost, (2) farmers, farm advisors, extension educators, nutrient management planners, crop advisors, nutritionists, state agency personnel, regulators, and university researchers need to be active participants in development of solutions, and (3) change to a sustainable future requires a combination of government regulation and outcome-based incentives.

•Agricultural green transformation of China requires restructuring of cropping systems.

Intensive agriculture in China over recent decades has successfully realized food security but at the expense of negative environmental impacts. Achieving green transformation of agriculture in China requires fundamental restructuring of cropping systems. This paper presents a theoretical framework of theory, approaches and implementation of crop diversification schemes in China. Initially, crop diversification schemes require identifying multiple objectives by simultaneously considering natural resources, limiting factors/constraints, and social and economic demands of different stakeholders. Then, it is necessary to optimize existing and/or design novel cropping systems based upon farming practices and ecological principles, and to strengthen targeted ecosystem services to achieve the identified objectives. Next, the resulting diversified cropping systems need to be evaluated and examined by employing experimental and modeling approaches. Finally, a strategic plan, as presented in this paper, is needed for implementing an optimized crop diversification in China based upon regional characteristics with the concurrent objectives of safe, nutritious food production and environmental protection. The North China Plain is used as an example to illustrate the strategic plan to optimize and design diversified cropping systems. The implementation of crop diversification in China will set an example for other countries undergoing agricultural transition, and contribute to global sustainable development.