Guangdong Academy of Agricultural Sciences

The impact of projected global warming on crop yields has been evaluated by indirect methods using simulation models. Direct studies on the effects of observed climate change on crop growth and yield could provide more accurate information for assessing the impact of climate change on crop production. We analyzed weather data at the International Rice Research Institute Farm from 1979 to 2003 to examine temperature trends and the relationship between rice yield and temperature by using data from irrigated field experiments conducted at the International Rice Research Institute Farm from 1992 to 2003. Here we report that annual mean maximum and minimum temperatures have increased by 0.35 degrees C and 1.13 degrees C, respectively, for the period 1979-2003 and a close linkage between rice grain yield and mean minimum temperature during the dry cropping season (January to April). Grain yield declined by 10% for each 1 degrees C increase in growing-season minimum temperature in the dry season, whereas the effect of maximum temperature on crop yield was insignificant. This report provides a direct evidence of decreased rice yields from increased nighttime temperature associated with global warming.

Microorganisms play an important role in soil phosphorus (P) cycling and regulation of P availability in agroecosystems. However, the responses of the functional and ecological traits of P-transformation microorganisms to long-term nutrient inputs are largely unknown. This study used metagenomics to investigate changes in the relative abundance of microbial P-transformation genes at four long-term experimental sites that received various inputs of N and P nutrients (up to 39 years). Long-term P input increased microbial P immobilization by decreasing the relative abundance of the P-starvation response gene (phoR) and increasing that of the low-affinity inorganic phosphate transporter gene (pit). This contrasts with previous findings that low-P conditions facilitate P immobilization in culturable microorganisms in short-term studies. In comparison, long-term nitrogen (N) input significantly decreased soil pH, and consequently decreased the relative abundances of total microbial P-solubilizing genes and the abundances of Actinobacteria, Gammaproteobacteria, and Alphaproteobacteria containing genes coding for alkaline phosphatase, and weakened the connection of relevant key genes. This challenges the concept that microbial P-solubilization capacity is mainly regulated by N:P stoichiometry. It is concluded that long-term N inputs decreased microbial P-solubilizing and mineralizing capacity while P inputs favored microbial immobilization via altering the microbial functional profiles, providing a novel insight into the regulation of P cycling in sustainable agroecosystems from a microbial perspective.

Tea is the world's oldest and most popular caffeine-containing beverage with immense economic, medicinal, and cultural importance. Here, we present the first high-quality nucleotide sequence of the repeat-rich (80.9%), 3.02-Gb genome of the cultivated tea tree Camellia sinensis. We show that an extraordinarily large genome size of tea tree is resulted from the slow, steady, and long-term amplification of a few LTR retrotransposon families. In addition to a recent whole-genome duplication event, lineage-specific expansions of genes associated with flavonoid metabolic biosynthesis were discovered, which enhance catechin production, terpene enzyme activation, and stress tolerance, important features for tea flavor and adaptation. We demonstrate an independent and rapid evolution of the tea caffeine synthesis pathway relative to cacao and coffee. A comparative study among 25 Camellia species revealed that higher expression levels of most flavonoid- and caffeine- but not theanine-related genes contribute to the increased production of catechins and caffeine and thus enhance tea-processing suitability and tea quality. These novel findings pave the way for further metabolomic and functional genomic refinement of characteristic biosynthesis pathways and will help develop a more diversified set of tea flavors that would eventually satisfy and attract more tea drinkers worldwide.

Abstract. A Nationwide Nitrogen Deposition Monitoring Network (NNDMN) containing 43 monitoring sites was established in China to measure gaseous NH3, NO2, and HNO3 and particulate NH4+ and NO3− in air and/or precipitation from 2010 to 2014. Wet/bulk deposition fluxes of Nr species were collected by precipitation gauge method and measured by continuous-flow analyzer; dry deposition fluxes were estimated using airborne concentration measurements and inferential models. Our observations reveal large spatial variations of atmospheric Nr concentrations and dry and wet/bulk Nr deposition. On a national basis, the annual average concentrations (1.3–47.0 μg N m−3) and dry plus wet/bulk deposition fluxes (2.9–83.3 kg N ha−1 yr−1) of inorganic Nr species are ranked by land use as urban > rural > background sites and by regions as north China > southeast China > southwest China > northeast China > northwest China > Tibetan Plateau, reflecting the impact of anthropogenic Nr emission. Average dry and wet/bulk N deposition fluxes were 20.6 ± 11.2 (mean ± standard deviation) and 19.3 ± 9.2 kg N ha−1 yr−1 across China, with reduced N deposition dominating both dry and wet/bulk deposition. Our results suggest atmospheric dry N deposition is equally important to wet/bulk N deposition at the national scale. Therefore, both deposition forms should be included when considering the impacts of N deposition on environment and ecosystem health.

BACKGROUND: The tuberous root of sweet potato is an important agricultural and biological organ. There are not sufficient transcriptomic and genomic data in public databases for understanding of the molecular mechanism underlying the tuberous root formation and development. Thus, high throughput transcriptome sequencing is needed to generate enormous transcript sequences from sweet potato root for gene discovery and molecular marker development. RESULTS: In this study, more than 59 million sequencing reads were generated using Illumina paired-end sequencing technology. De novo assembly yielded 56,516 unigenes with an average length of 581 bp. Based on sequence similarity search with known proteins, a total of 35,051 (62.02%) genes were identified. Out of these annotated unigenes, 5,046 and 11,983 unigenes were assigned to gene ontology and clusters of orthologous group, respectively. Searching against the Kyoto Encyclopedia of Genes and Genomes Pathway database (KEGG) indicated that 17,598 (31.14%) unigenes were mapped to 124 KEGG pathways, and 11,056 were assigned to metabolic pathways, which were well represented by carbohydrate metabolism and biosynthesis of secondary metabolite. In addition, 4,114 cDNA SSRs (cSSRs) were identified as potential molecular markers in our unigenes. One hundred pairs of PCR primers were designed and used for validation of the amplification and assessment of the polymorphism in genomic DNA pools. The result revealed that 92 primer pairs were successfully amplified in initial screening tests. CONCLUSION: This study generated a substantial fraction of sweet potato transcript sequences, which can be used to discover novel genes associated with tuberous root formation and development and will also make it possible to construct high density microarrays for further characterization of gene expression profiles during these processes. Thousands of cSSR markers identified in the present study can enrich molecular markers and will facilitate marker-assisted selection in sweet potato breeding. Overall, these sequences and markers will provide valuable resources for the sweet potato community. Additionally, these results also suggested that transcriptome analysis based on Illumina paired-end sequencing is a powerful tool for gene discovery and molecular marker development for non-model species, especially those with large and complex genome.

Chlorogenic acids (CGAs), a group of hydroxycinnamates, are generally abundant in everyday foods and beverages, most prominently in certain coffee drinks. Among them, the chlorogenic acid (CGA), also termed as 5-O-caffeoylquinic acid (5-CQA), is one of the most abundant, highly functional polyphenolic compounds in the human diet. The evidence of its health benefits obtained from clinical studies, as well as basic research, indicates an inverse correlation between 5-CQA consumption and a lower risk of metabolic syndromes and chronic diseases. This review focuses on the beneficial properties for health and mechanisms of action of 5-CQA, starting with its history, isomers, dietary sources, processing effects, preparation methods, pharmacological safety evaluation, and bioavailability. It also provides the possible molecular mechanistic bases to explain the health beneficial effects of 5-CQA including neuroprotective, cardiovascular protective, gastrointestinal protective, renoprotective, hepatoprotective, glucose and lipid metabolism regulatory, and anticarcinogenic effects. The information summarized here could aid in the basic and clinical research on 5-CQA as a natural dietary additive, potential drug candidate, as well as a natural health promoter.

The outbreak of a novel corona Virus Disease 2019 (COVID-19) in the city of Wuhan, China has resulted in more than 1.7 million laboratory confirmed cases all over the world. Recent studies showed that SARS-CoV-2 was likely originated from bats, but its intermediate hosts are still largely unknown. In this study, we assembled the complete genome of a coronavirus identified in 3 sick Malayan pangolins. The molecular and phylogenetic analyses showed that this pangolin coronavirus (pangolin-CoV-2020) is genetically related to the SARS-CoV-2 as well as a group of bat coronaviruses but do not support the SARS-CoV-2 emerged directly from the pangolin-CoV-2020. Our study suggests that pangolins are natural hosts of Betacoronaviruses. Large surveillance of coronaviruses in pangolins could improve our understanding of the spectrum of coronaviruses in pangolins. In addition to conservation of wildlife, minimizing the exposures of humans to wildlife will be important to reduce the spillover risks of coronaviruses from wild animals to humans.

Increased consumption of whole grains has been associated with reduced risk of developing major chronic diseases. These health benefits have been attributed in part to their unique phytochemicals. Previous studies on black rice mainly focused on anthocyanins. Little is known about the phytochemical profiles and antioxidant activities of different black rice varieties. The objective of this study was to determine the phytochemical profiles and antioxidant activity of rice bran samples from 12 diverse varieties of black rice. The free, bound, and total phenolic contents of black rice bran samples ranged from 2086 to 7043, from 221.2 to 382.7, and from 2365 to 7367 mg of gallic acid equiv/100 g of dry weight (DW), respectively. The percentage contribution of free phenolics to the total ranged from 88.2 to 95.6%. The average values of free, bound, and total phenolic contents of black rice bran were 8, 1.5, and 6 times higher than those of white rice bran, respectively (p < 0.05). The free, bound, and total flavonoid contents of black rice bran samples ranged from 3462 to 12061, from 126.7 to 386.9, and from 3596 to 12448 mg of catechin equiv/100 g of DW, respectively. The percentage contribution of free flavonoids to the total ranged from 96.3 to 97.6%. The average values of free, bound, and total flavonoid contents of black rice bran were 7.4, 1.9, and 6.7 times higher than those of white rice bran, respectively (p < 0.05). The free, bound, and total anthocyanin contents of black rice bran samples ranged from 1227 to 5096, from 4.89 to 8.23, and from 1231 to 5101 mg of cyanidin-3-glucoside equiv/100 g of DW, respectively. The percentage contribution of free anthocyanins to the total ranged from 99.5 to 99.9%. Cyanidin-3-glucoside, cyanidin-3-rutinoside, and peonidin-3-glucoside were detected in black rice bran samples and ranged from 736.6 to 2557, from 22.70 to 96.62, and from 100.7 to 534.2 mg/100 g of DW, respectively. The free, bound, and total antioxidant activities of black rice bran samples ranged from 476.9 to 180, from 47.91 to 79.48, and from 537.5 to 1876 mumol of Trolox equiv/g of DW, respectively. The percentage contribution of free antioxidant activity to the total ranged from 88.7 to 96.0%. The average values of free, bound, and total antioxidant activity of black rice bran were more than 8, 1.5, and 6 times higher than those of white rice bran, respectively (p < 0.05). The total antioxidant activity of black rice bran was correlated to the content of total phenolics, total flavonoids, and total anthocyanins and also was significantly correlated to the contents of cyanidin-3-glucoside, cyanidin-3-rutinoside, and peonidin-3-glucoside. These results indicate that there are significant differences in phytochemical content and antioxidant activity among the different black rice varieties. Black rice bran has higher content of phenolics, flavonoids, and anthocyanins and has higher antioxidant activity when compared to white rice bran. Interestingly, the phenolics, flavonoids, and anthocyanins of black rice bran are mainly present in free form. Knowing the phytochemical profile and antioxidant activity of black rice bran gives insights to its potential application to promote health.

Bacterial wilt caused by plant pathogenic Ralstonia spp. is one of the most important diseases affecting the production of many important crops worldwide. In China, a large scientific community has been dedicated to studying bacterial wilt and its causative agent, R. pseudosolanacearum and R. solanacearum. Most of their work was published in Chinese, which has hindered international communication and collaboration in this field. In this review, we summarize the status of knowledge on geographical distribution, diversity, and host range of Ralstonia spp., as well as, the impact of bacterial wilt on important crops and disease control approaches, in China. We present areas of research and publications by Chinese scientists and propose the promotion of collaborative research within China and with the international community.

Human utilization of the mulberry–silkworm interaction started at least 5,000 years ago and greatly influenced world history through the Silk Road. Complementing the silkworm genome sequence, here we describe the genome of a mulberry species Morus notabilis. In the 330-Mb genome assembly, we identify 128 Mb of repetitive sequences and 29,338 genes, 60.8% of which are supported by transcriptome sequencing. Mulberry gene sequences appear to evolve ~3 times faster than other Rosales, perhaps facilitating the species’ spread worldwide. The mulberry tree is among a few eudicots but several Rosales that have not preserved genome duplications in more than 100 million years; however, a neopolyploid series found in the mulberry tree and several others suggest that new duplications may confer benefits. Five predicted mulberry miRNAs are found in the haemolymph and silk glands of the silkworm, suggesting interactions at molecular levels in the plant–herbivore relationship. The identification and analyses of mulberry genes involved in diversifying selection, resistance and protease inhibitor expressed in the laticifers will accelerate the improvement of mulberry plants. Mulberry trees are the primary food source for silkworms, which are reared for the production of silk. In this study, He et al. present the draft genome sequence of Morus notabilisand find that it evolved significantly faster than other plants in the Rosales order.

Heavy metal (HM) pollution of soils is a globally important ecological and environmental problem. Previous studies have focused on i) tracking pollution sources in HM-contaminated soils, ii) exploring the adsorption capacity and distribution of HMs, and iii) assessing phyto-uptake of HMs and their ecotoxicity. However, few reviews have systematically summarized HM pollution in soil-plant systems over the past decade. Understanding the mechanisms of interaction between HMs and solid soil components is consequently key to effectively controlling and remediating HM pollution. However, the compositions of solid soil phases are diverse, their structures are complex, and their spatial arrangements are heterogeneous, all leading to the formation of soil micro-domains that exhibit different particle sizes and surface properties. The various soil components and their interactions ultimately control the speciation, transformation, and bioavailability of HMs in soils. Over the past few decades, the extensive application of advanced instrumental techniques and methods has greatly expanded our understanding of the behavior of HMs in organic mineral assemblages. In this review, studies investigating the immobilization of HMs by minerals, organic compounds, microorganisms, and their associated complexes are summarized, with a particular emphasis on the interfacial adsorption and immobilization of HMs. In addition, methods for analyzing the speciation and distribution of HMs in aggregates of natural soils with different particle sizes are also discussed. Moreover, we also review the methods for speciating HMs at mineral-organic micro-scale interfaces. Lastly, developmental prospects for HM research at inorganic-organic interfaces are outlined. In future research, the most advanced methods should be used to characterize the interfaces and in situ characteristics of metals and metal complexes. In particular, the roles and contributions of microorganisms in the immobilization of HMs at complex mineral-organic interfaces require significant further investigation.

Phytohormones (PHs) play crucial role in regulation of various physiological and biochemical processes that govern plant growth and yield under optimal and stress conditions. The interaction of these PHs is crucial for plant survival under stressful environments as they trigger signaling pathways. Hormonal cross regulation initiate a cascade of reactions which finely tune the physiological processes in plant architecture that help plant to grow under suboptimal growth conditions. Recently, various studies have highlighted the role of PHs such as abscisic acid, salicylic acid, ethylene, and jasmonates in the plant responses toward environmental stresses. The involvement of cytokinins, gibberellins, auxin, and relatively novel PHs such as strigolactones and brassinosteroids in plant growth and development has been documented under normal and stress conditions. The recent identification of the first plant melatonin receptor opened the door to this regulatory molecule being considered a new plant hormone. However, polyamines, which are not considered PHs, have been included in this chapter. Various microbes produce and secrete hormones which helped the plants in nutrient uptake such as N, P, and Fe. Exogenous use of such microbes help plants in correcting nutrient deficiency under abiotic stresses. This chapter focused on the recent developments in the knowledge related to PHs and their involvement in abiotic stresses of anticipation, signaling, cross-talk, and activation of response mechanisms. In view of role of hormones and capability of microbes in producing hormones, we propose the use of hormones and microbes as potential strategy for crop stress management.

Advances in next-generation sequencing and genotyping technologies have enabled generation of large-scale genomic resources such as molecular markers, transcript reads and BAC-end sequences (BESs) in chickpea, pigeonpea and groundnut, three major legume crops of the semi-arid tropics. Comprehensive transcriptome assemblies and genome sequences have either been developed or underway in these crops. Based on these resources, dense genetic maps, QTL maps as well as physical maps for these legume species have also been developed. As a result, these crops have graduated from 'orphan' or 'less-studied' crops to 'genomic resources rich' crops. This article summarizes the above-mentioned advances in genomics and genomics-assisted breeding applications in the form of marker-assisted selection (MAS) for hybrid purity assessment in pigeonpea; marker-assisted backcrossing (MABC) for introgressing QTL region for drought-tolerance related traits, Fusarium wilt (FW) resistance and Ascochyta blight (AB) resistance in chickpea; late leaf spot (LLS), leaf rust and nematode resistance in groundnut. We critically present the case of use of other modern breeding approaches like marker-assisted recurrent selection (MARS) and genomic selection (GS) to utilize the full potential of genomics-assisted breeding for developing superior cultivars with enhanced tolerance to various environmental stresses. In addition, this article recommends the use of advanced-backcross (AB-backcross) breeding and development of specialized populations such as multi-parents advanced generation intercross (MAGIC) for creating new variations that will help in developing superior lines with broadened genetic base. In summary, we propose the use of integrated genomics and breeding approach in these legume crops to enhance crop productivity in marginal environments ensuring food security in developing countries.

Plastic pollution is a global concern given its prevalence in aquatic and terrestrial ecosystems. Studies have been conducted on the distribution and impact of plastic pollution in marine ecosystems, but little is known on terrestrial ecosystems. Plastic mulch has been widely used to increase crop yields worldwide, yet the impact of plastic residues in cropland soils to soil health and crop production in the long term remained unclear. In this paper, using a global meta-analysis, we found that the use of plastic mulch can indeed increase crop yields on average by 25%-42% in the immediate season due to the increase of soil temperature (+8%) and moisture (+17%). However, the unabated accumulation of film residues in the field negatively impacts its physicochemical properties linked to healthy soil and threatens food production in the long term. It has multiple negative impacts on plant growth including crop yield (at the mean rate of -3% for every additional 100 kg/ha of film residue), plant height (-2%) and root weight (-5%), and soil properties including soil water evaporation capacity (-2%), soil water infiltration rate (-8%), soil organic matter (-0.8%) and soil available phosphorus (-5%) based on meta-regression. Using a nationwide field survey of China, the largest user of plastic mulch worldwide, we found that plastic residue accumulation in cropland soils has reached 550,800 tonnes, with an estimated 6%-10% reduction in cotton yield in some polluted sites based on current level of plastic residue content. Immediate actions should be taken to ensure the recovery of plastic film mulch and limit further increase in film residue loading to maintain the sustainability of these croplands.

Metabolites from intestinal microbes modulate the mucosal immune system by regulating the polarization and expansion of T cells. Whether the microbial metabolites influence macrophage polarization, however, is poorly understood. Here, we show that the large bowel microbial fermentation product, butyrate, facilitates M2 macrophage polarization, in vitro and in vivo. The supernatant from butyrate-treated M2 macrophage increased the migration and enhanced the wound closure rate of MLE-12 cells. Butyrate attenuated intestinal inflammation in mice with dextran sulfate sodium (DSS)-induced colitis, with a significant increase in colonic expression of the M2 macrophage-associated protein, Arg1. M2 macrophage treated with butyrate, had increased activation of the H3K9/STAT6 signaling pathway, suggesting a mechanism for butyrate facilitated M2 macrophage polarization. Collectively, our study indicated that commensal microbe-derived butyrate is a novel activator of STAT6-mediated transcription through H3K9 acetylation driving M2 macrophage polarization, and delineated new insights into the immune interplay underlying inflammatory bowel disease.

The reductive dechlorination of pentachlorophenol (PCP) by Geobacter sulfurreducens in the presence of different biochars was investigated to understand how biochars affect the bioreduction of environmental contaminants. The results indicated that biochars significantly accelerate electron transfer from cells to PCP, thus enhancing reductive dechlorination. The promotion effects of biochar (as high as 24-fold) in this process depend on its electron exchange capacity (EEC) and electrical conductivity (EC). A kinetic model revealed that the surface redox-active moieties (RAMs) and EC of biochar (900 °C) contributed to 56% and 41% of the biodegradation rate, respectively. This work demonstrates that biochars are efficient electron mediators for the dechlorination of PCP and that both the EC and RAMs of biochars play important roles in the electron transfer process.

Feed protein supplements are one of the most expensive and limiting feed ingredients. This review offers a comprehensive analysis of how the expected expansion of animal production, driven by the rising world population and living standards for more animal-sourced foods, is creating a global shortage of feed protein supply. Because ruminants, chickens, and pigs contribute to 96% of the global supply of animal protein and aquaculture is growing fast, means of meeting the feed protein requirements of these species are elaborated. Geographic variation and interdependence among China, Europe, and North America in the demand and supply of feed protein are compared. The potential and current state of exploration into alternative feed proteins, including microalgae, insects, single-cell proteins, and coproducts, are highlighted. Strategic innovations are proposed to upgrade feed protein processing and assessment, improve protein digestion by exogenous enzymes, and genetically select feed-efficient livestock breeds. An overall successful and sustainable solution in meeting global feed protein demands will lead to a substantial net gain of human-edible animal protein with a minimal environmental footprint.

Rice (Oryza sativa L.) blast disease caused by Magnaporthe grisea is one of the most destructive diseases in the rice-growing areas of the world. Silicon is an important nutritional element especially for rice. Two near-isogenic lines of rice with different resistance to blast disease, i.e. CO39 (susceptible) and C101LAC (Pi-1) (resistant), were selected to determine the effects of Si amendment on the severity and incidence of rice blast disease. The physiological and cytological mechanisms involved in the induced disease resistance by silicon were investigated. Exogenous Si application at a concentration of 2 mM reduced the disease index by 45% for CO39 and 56% for C101LAC (Pi-1). Si application alone did not change lignin content and the activities of defense-related enzymes including peroxidase (POD), polyphenol oxidase (PPO) and phenylalanine ammonia-lyase (PAL) in rice leaves of both isogenic lines. However, after inoculation with M. grisea, Si-treated rice plants significantly increased the activities of POD, PPO and PAL in leaves of both isogenic lines. Si and lignin content were also significantly increased in Si-treated inoculated seedlings. Environmental scanning electron microscope observations revealed that Si amendment resulted in higher Si deposit on dumbbell bodies in the rice leaves and silicon papilla accumulation on the guard cell of stoma. These results suggest that silicon-induced defense response and cell silicification of rice leaves altogether contribute to the silicon-induced rice resistance to blast disease.

Peanut genomics is very challenging due to its inherent problem of genetic architecture. Blockage of gene flow from diploid wild relatives to the tetraploid; cultivated peanut, recent polyploidization combined with self pollination, and the narrow genetic base of the primary genepool have resulted in low genetic diversity that has remained a major bottleneck for genetic improvement of peanut. Harnessing the rich source of wild relatives has been negligible due to differences in ploidy level as well as genetic drag and undesirable alleles for low yield. Lack of appropriate genomic resources has severely hampered molecular breeding activities, and this crop remains among the less-studied crops. The last five years, however, have witnessed accelerated development of genomic resources such as development of molecular markers, genetic and physical maps, generation of expressed sequenced tags (ESTs), development of mutant resources, and functional genomics platforms that facilitate the identification of QTLs and discovery of genes associated with tolerance/resistance to abiotic and biotic stresses and agronomic traits. Molecular breeding has been initiated for several traits for development of superior genotypes. The genome or at least gene space sequence is expected to be available in near future and this will further accelerate use of biotechnological approaches for peanut improvement.

The diamondback moth (DBM), Plutella xylostella (L.), costs the Chinese economy US$0.77 billion annually, and considerable research has focused on its biology, ecology, and management. Much of this research has been published locally and is inaccessible outside China. Since 1990 Brassica vegetable production has increased 20-fold and production practices have intensified, but losses continue to increase. Insecticide use is widespread and many DBM populations, particularly in southern provinces, are resistant to multiple compounds. The molecular bases of several insecticide resistance mechanisms are well understood, and genetic studies suggest that insecticide-resistant populations migrate northward in spring and that back migrations may occur in southern provinces. Fundamental studies have improved our understanding of the effects of temperature on DBM population dynamics and distributions and of interactions between DBM and its well-established parasitoid fauna. Nationally coordinated research is developing regional management strategies that integrate locally appropriate biological, physical, cultural, and insecticidal control, but sustaining their adoption will prove an enormous challenge.