Shandong Academy of Agricultural Sciences

This paper reports the genome sequence of domesticated tomato, a major crop plant, and a draft sequence for its closest wild relative; comparative genomics reveal very little divergence between the two genomes but some important differences with the potato genome, another important food crop in the genus Solanum. Tomato (Solanum lycopersicum) is a major crop plant and a model system for fruit development. Solanum is one of the largest angiosperm genera1 and includes annual and perennial plants from diverse habitats. Here we present a high-quality genome sequence of domesticated tomato, a draft sequence of its closest wild relative, Solanum pimpinellifolium2, and compare them to each other and to the potato genome (Solanum tuberosum). The two tomato genomes show only 0.6% nucleotide divergence and signs of recent admixture, but show more than 8% divergence from potato, with nine large and several smaller inversions. In contrast to Arabidopsis, but similar to soybean, tomato and potato small RNAs map predominantly to gene-rich chromosomal regions, including gene promoters. The Solanum lineage has experienced two consecutive genome triplications: one that is ancient and shared with rosids, and a more recent one. These triplications set the stage for the neofunctionalization of genes controlling fruit characteristics, such as colour and fleshiness.

Potato (Solanum tuberosum L.) is the world’s most important non-grain food crop and is central to global food security. It is clonally propagated, highly heterozygous, autotetraploid, and suffers acute inbreeding depression. Here we use a homozygous doubled-monoploid potato clone to sequence and assemble 86% of the 844-megabase genome. We predict 39,031 protein-coding genes and present evidence for at least two genome duplication events indicative of a palaeopolyploid origin. As the first genome sequence of an asterid, the potato genome reveals 2,642 genes specific to this large angiosperm clade. We also sequenced a heterozygous diploid clone and show that gene presence/absence variants and other potentially deleterious mutations occur frequently and are a likely cause of inbreeding depression. Gene family expansion, tissue-specific expression and recruitment of genes to new pathways contributed to the evolution of tuber development. The potato genome sequence provides a platform for genetic improvement of this vital crop. The genome of the potato (Solanum tuberosum L.), a staple crop vital to food security, has been sequenced. The Potato Genome Sequencing Consortium sequenced a homozygous doubled-monoploid potato clone as well as a heterozygous diploid clone. Genome analysis reveals traces of at least two genome duplication events and genes specific to Asterids, a large clade of flowering plants of which the potato is the first to be sequenced. Gene presence/absence variants and other potentially deleterious mutations are frequent and may be the cause of inbreeding depression. The genome sequence will facilitate genetic improvements in the potato with a view to improving yield and to increasing disease and stress resistance of this crop, which is a now a significant component of worldwide food production and is becoming increasingly important in the developing world.

High oil and protein content make tetraploid peanut a leading oil and food legume. Here we report a high-quality peanut genome sequence, comprising 2.54 Gb with 20 pseudomolecules and 83,709 protein-coding gene models. We characterize gene functional groups implicated in seed size evolution, seed oil content, disease resistance and symbiotic nitrogen fixation. The peanut B subgenome has more genes and general expression dominance, temporally associated with long-terminal-repeat expansion in the A subgenome that also raises questions about the A-genome progenitor. The polyploid genome provided insights into the evolution of Arachis hypogaea and other legume chromosomes. Resequencing of 52 accessions suggests that independent domestications formed peanut ecotypes. Whereas 0.42-0.47 million years ago (Ma) polyploidy constrained genetic variation, the peanut genome sequence aids mapping and candidate-gene discovery for traits such as seed size and color, foliar disease resistance and others, also providing a cornerstone for functional genomics and peanut improvement.

Fungal disease meets its match Fusarium head blight (FHB), caused by a fungus, reduces wheat crop yield and introduces toxins into the harvest. From the assembly of the genome of Thinopyrum elongatum , a wild relative of wheat used in breeding programs to improve cultivated wheat, Wang et al. cloned a gene that can address both problems (see the Perspective by Wulff and Jones). The encoded glutathione S -transferase detoxifies the trichothecene toxin and, when expressed in wheat, confers resistance to FHB. Science , this issue p. eaba5435 ; see also p. 822

Colistin represents one of the few available drugs for treating infections caused by carbapenem-resistant Enterobacteriaceae. As such, the recent plasmid-mediated spread of the colistin resistance gene mcr-1 poses a significant public health threat, requiring global monitoring and surveillance. Here, we characterize the global distribution of mcr-1 using a data set of 457 mcr-1-positive sequenced isolates. We find mcr-1 in various plasmid types but identify an immediate background common to all mcr-1 sequences. Our analyses establish that all mcr-1 elements in circulation descend from the same initial mobilization of mcr-1 by an ISApl1 transposon in the mid 2000s (2002-2008; 95% highest posterior density), followed by a marked demographic expansion, which led to its current global distribution. Our results provide the first systematic phylogenetic analysis of the origin and spread of mcr-1, and emphasize the importance of understanding the movement of antibiotic resistance genes across multiple levels of genomic organization.

In modern society, traffic and transportation and the manufacturing industry and construction industries continuously release large amounts of dust and particles into the atmosphere, which can cause heavy air pollution, leading to health hazards. The haze disaster, a serious problem in developing countries such as China and India, has become one of the main issues of global environmental pollution in recent decades. Many air filtration technologies have been developed. Air filtration using electrospun fibers that intercept fine particles/volatile organic gases/bacterium is a relatively new, but highly promising, technique. Due to their interconnected nanoscale pore structures, highly specific surface areas, fine diameters, and porous structure as well as their ability to incorporate active chemistry on a nanoscale surface, electrospun fibers are becoming a promising versatile platform for air filtration. In this review, following a short introduction concerning the need for air filtration and filtration theory and mechanism, electrospun nanofibers membranes for air filtration have been highlighted, including the preparation (electrospinning process) and the parameters relevant to filtration efficacy. Additionally, various types (function) of the electrospun air filtration membranes have been classified in detail. Furthermore, their potential in the filtration of fine particles and chemical pollutants has been discussed. Finally, the challenges of their practical application and the future prospects have been summarized. Given that some advanced electrospun air filtration nanofibrous membranes exist for treating different contaminants from various types of polluted atmosphere, it is believed that they should make a significant contribution in protection against air pollution.

Abstract Missing heritability in genome-wide association studies defines a major problem in genetic analyses of complex biological traits 1,2 . The solution to this problem is to identify all causal genetic variants and to measure their individual contributions 3,4 . Here we report a graph pangenome of tomato constructed by precisely cataloguing more than 19 million variants from 838 genomes, including 32 new reference-level genome assemblies. This graph pangenome was used for genome-wide association study analyses and heritability estimation of 20,323 gene-expression and metabolite traits. The average estimated trait heritability is 0.41 compared with 0.33 when using the single linear reference genome. This 24% increase in estimated heritability is largely due to resolving incomplete linkage disequilibrium through the inclusion of additional causal structural variants identified using the graph pangenome. Moreover, by resolving allelic and locus heterogeneity, structural variants improve the power to identify genetic factors underlying agronomically important traits leading to, for example, the identification of two new genes potentially contributing to soluble solid content. The newly identified structural variants will facilitate genetic improvement of tomato through both marker-assisted selection and genomic selection. Our study advances the understanding of the heritability of complex traits and demonstrates the power of the graph pangenome in crop breeding.

Human selection has reshaped crop genomes. Here we report an apple genome variation map generated through genome sequencing of 117 diverse accessions. A comprehensive model of apple speciation and domestication along the Silk Road is proposed based on evidence from diverse genomic analyses. Cultivated apples likely originate from Malus sieversii in Kazakhstan, followed by intensive introgressions from M. sylvestris. M. sieversii in Xinjiang of China turns out to be an "ancient" isolated ecotype not directly contributing to apple domestication. We have identified selective sweeps underlying quantitative trait loci/genes of important fruit quality traits including fruit texture and flavor, and provide evidences supporting a model of apple fruit size evolution comprising two major events with one occurring prior to domestication and the other during domestication. This study outlines the genetic basis of apple domestication and evolution, and provides valuable information for facilitating marker-assisted breeding and apple improvement.Apple is one of the most important fruit crops. Here, the authors perform deep genome resequencing of 117 diverse accessions and reveal comprehensive models of apple origin, speciation, domestication, and fruit size evolution as well as candidate genes associated with important agronomic traits.

The root microbiome refers to the community of microbes living in association with a plant's roots, and includes mutualists, pathogens, and commensals. Here we focus on recent advances in the study of root commensal community which is the major research object of microbiome-related researches. With the rapid development of new technologies, plant-commensal interactions can be explored with unprecedented breadth and depth. Both the soil environment and the host plant drive commensal community assembly. The bulk soil is the seed bank of potential commensals, and plants use root exudates and immune responses to build healthy microbial communities from the available microbes. The plant microbiome extends the functional system of plants by participating in a variety of processes, including nutrient absorption, growth promotion, and resistance to biotic and abiotic stresses. Plants and their microbiomes have evolved adaptation strategies over time. However, there is still a huge gap in our understanding of the regulatory mechanisms of plant-commensal interactions. In this review, we summarize recent research on the assembly of root microbial communities and the effects of these communities on plant growth and development, and look at the prospects for promoting sustainable agricultural development through the study of the root microbiome.

We have recently reported the isolation of a novel virus, provisionally designated C/swine/Oklahoma/1334/2011 (C/OK), with 50% overall homology to human influenza C viruses (ICV), from a pig in Oklahoma. Deep RNA sequencing of C/OK virus found a matrix 1 (M1) protein expression strategy that differed from that of ICV. The novelty of C/OK virus prompted us to investigate whether C/OK virus could exist in a nonswine species. Significantly, we found that C/OK virus was widespread in U.S. bovine herds, as demonstrated by reverse transcription (RT)-PCR and serological assays. Genome sequencing of three bovine viruses isolated from two herds in different states further confirmed these findings. To determine whether swine/bovine C/OK viruses can undergo reassortment with human ICV, and to clarify the taxonomic status of C/OK, in vitro reassortment and serological typing by agar gel immunodiffusion (AGID) were conducted. In vitro reassortment using two human ICV and two swine and bovine C/OK viruses demonstrated that human ICV and C/OK viruses were unable to reassort and produce viable progeny. Antigenically, no cross-recognition of detergent split virions was observed in AGID between human and nonhuman viruses by using polyclonal antibodies that were reactive to cognate antigens. Taken together, these results demonstrate that C/OK virus is genetically and antigenically distinct from ICV. The classification of the new virus in a separate genus of the Orthomyxoviridae family is proposed. The finding of C/OK virus in swine and bovine indicates that this new virus may spread and establish infection in other mammals, including humans. IMPORTANCE Influenza C viruses (ICV) are common human pathogens, infecting most people during childhood and adolescence, and typically cause mild respiratory symptoms. While ICV have been isolated from both pigs and dogs, humans are thought to be the natural viral reservoir. Previously, we characterized an ICV-like virus isolated from pigs exhibiting symptoms of influenza virus-like illness. Here, we show molecular and serological data demonstrating widespread circulation of similar viruses in bovines. Deep RNA sequencing, phylogenetic analysis, and in vitro reassortment experiments demonstrate that animal ICV-like viruses are genetically distinct from human ICV. Antigenically, we show that ICV-like viruses are not recognized by ICV antibodies. En masse, these results suggest that bovine influenza virus warrants classification as a new genus of influenza virus. The finding of this novel virus that can infect multiple mammalian species warrants further research into its role in human health.

Domestication of the apple was mainly driven by interspecific hybridization. In the present study, we report the haplotype-resolved genomes of the cultivated apple (Malus domestica cv. Gala) and its two major wild progenitors, M. sieversii and M. sylvestris. Substantial variations are identified between the two haplotypes of each genome. Inference of genome ancestry identifies ~23% of the Gala genome as of hybrid origin. Deep sequencing of 91 accessions identifies selective sweeps in cultivated apples that originated from either of the two progenitors and are associated with important domestication traits. Construction and analyses of apple pan-genomes uncover thousands of new genes, with hundreds of them being selected from one of the progenitors and largely fixed in cultivated apples, revealing that introgression of new genes/alleles is a hallmark of apple domestication through hybridization. Finally, transcriptome profiles of Gala fruits at 13 developmental stages unravel ~19% of genes displaying allele-specific expression, including many associated with fruit quality.

Cotton (Gossypium hirsutum L.) production in China has developed rapidly during the last 60 years. In 2012, the planting area and total output in the country were 5.3 million hectares and 7.62 million tons, respectively, and the unit yield was 85% higher than the world average. China currently accounts for about 30% of the world's cotton output with only 15% of the world's cotton land. Enhanced cotton production, particularly the high unit yield is largely due to adoption of a series of intensive farming technologies and cultural practices. The intensive farming technologies for cotton production in China mainly include seedling transplanting, plastic mulching, double cropping, plant training and super-high plant density technique, which have played important roles in promoting unit yield and total output. Although such intensive farming technologies meet the need of a growing population under limited arable land in China, they are labor-intensive and involve large input of various kinds of chemical products like fertilizers, pesticides, and plastic films. Thus, there are increasing challenges from soil pollution and labor shortage. Here, the achievements, challenges, countermeasures and prospects for intensive cotton cultivation in China are reviewed. An important conclusion from this review is that the establishment of a new farming technology through reform of the current intensive technology is inevitable to support sustainable cotton production in the nation. A series of comprehensive countermeasures should be taken to reduce soil pollution through rational use of plastic film and chemicals, labor saving through simplifying field managements and mechanization and increasing benefits by reforming the cropping system and management mode. China's cotton production would be sustainable with a bright prospect if supported by new farming technologies.

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.

Peanut or groundnut (Arachis hypogaea L.), a legume of South American origin, has high seed oil content (45-56%) and is a staple crop in semiarid tropical and subtropical regions, partially because of drought tolerance conferred by its geocarpic reproductive strategy. We present a draft genome of the peanut A-genome progenitor, Arachis duranensis, and 50,324 protein-coding gene models. Patterns of gene duplication suggest the peanut lineage has been affected by at least three polyploidizations since the origin of eudicots. Resequencing of synthetic Arachis tetraploids reveals extensive gene conversion in only three seed-to-seed generations since their formation by human hands, indicating that this process begins virtually immediately following polyploid formation. Expansion of some specific gene families suggests roles in the unusual subterranean fructification of Arachis For example, the S1Fa-like transcription factor family has 126 Arachis members, in contrast to no more than five members in other examined plant species, and is more highly expressed in roots and etiolated seedlings than green leaves. The A. duranensis genome provides a major source of candidate genes for fructification, oil biosynthesis, and allergens, expanding knowledge of understudied areas of plant biology and human health impacts of plants, informing peanut genetic improvement and aiding deeper sequencing of Arachis diversity.

The genome of potato, a major global food crop, was recently sequenced. The work presented here details the integration of the potato reference genome (DM) with a new sequence-tagged site marker-based linkage map and other physical and genetic maps of potato and the closely related species tomato. Primary anchoring of the DM genome assembly was accomplished by the use of a diploid segregating population, which was genotyped with several types of molecular genetic markers to construct a new ~936 cM linkage map comprising 2469 marker loci. In silico anchoring approaches used genetic and physical maps from the diploid potato genotype RH89-039-16 (RH) and tomato. This combined approach has allowed 951 superscaffolds to be ordered into pseudomolecules corresponding to the 12 potato chromosomes. These pseudomolecules represent 674 Mb (~93%) of the 723 Mb genome assembly and 37,482 (~96%) of the 39,031 predicted genes. The superscaffold order and orientation within the pseudomolecules are closely collinear with independently constructed high density linkage maps. Comparisons between marker distribution and physical location reveal regions of greater and lesser recombination, as well as regions exhibiting significant segregation distortion. The work presented here has led to a greatly improved ordering of the potato reference genome superscaffolds into chromosomal "pseudomolecules".

Although humic acid has been demonstrated to improve the quality of some soil types, the long-term effects of humic acid on soil under continuous cropping peanut are not fully understood. This study aimed to investigate the continuous effects of humic acid on the physicochemical properties, microbial diversity, and enzyme activities of soil under continuous cropping peanut. In this study, a three-year consecutive experiment of cropping peanut was conducted in the North China Plain. In addition to the equal nitrogen, phosphorus, and potassium inputs, humic acid treatment was applied with inorganic fertilizers. Compared with control experiments, humic acid increased the yield and quality of continuous cropping peanut. To elucidate the mechanism of humic acid affecting the soil quality, various soil quality indicators were evaluated and compared in this study. It was found that humic acid increased soil nutrient contents, including the total soil nitrogen, total phosphorus, total potassium, available nitrogen, available phosphorus, available potassium, and organic matter contents, which exhibited the maximum effect in the third year. Meanwhile, the urease, sucrase, and phosphatase activities in the soil significantly increased after treated with humic acid, of which the maturity period increased most significantly. The same results were observed for three consecutive years. Microbial diversity varied considerably according to the high throughput sequencing analysis. Specifically, the number of bacteria decreased while that of fungi increased after humic acid treatment. The abundance of Firmicutes in bacteria, Basidiomycota, and Mortierellomycota in fungi all increased, which have been reported as being beneficial to plant growth. In contrast, the abundance of Ascomycota in fungi was reduced, and most of the related genera identified are pathogenic to plants. In conclusion, humic acid improved the yield and quality of continuous cropping peanut because of improved physicochemical properties, enzymatic activities, and microbial diversity of soil, which is beneficial for alleviating the obstacles of continuous cropping peanut.

BACKGROUND: MicroRNAs (miRNAs) are a new class of small, endogenous RNAs that play a regulatory role in the cell by negatively affecting gene expression at the post-transcriptional level. miRNAs have been shown to control numerous genes involved in various biological and metabolic processes. There have been extensive studies on discovering miRNAs and analyzing their functions in model species, such as Arabidopsis and rice. Increasing investigations have been performed on important agricultural crops including soybean, conifers, and Phaselous vulgaris but no studies have been reported on discovering peanut miRNAs using a cloning strategy. RESULTS: In this study, we employed the next generation high through-put Solexa sequencing technology to clone and identify both conserved and species-specific miRNAs in peanuts. Next generation high through-put Solexa sequencing showed that peanuts have a complex small RNA population and the length of small RNAs varied, 24-nt being the predominant length for a majority of the small RNAs. Combining the deep sequencing and bioinformatics, we discovered 14 novel miRNA families as well as 75 conserved miRNAs in peanuts. All 14 novel peanut miRNAs are considered to be species-specific because no homologs have been found in other plant species except ahy-miRn1, which has a homolog in soybean. qRT-PCR analysis demonstrated that both conserved and peanut-specific miRNAs are expressed in peanuts. CONCLUSIONS: This study led to the discovery of 14 novel and 22 conserved miRNA families from peanut. These results show that regulatory miRNAs exist in agronomically important peanuts and may play an important role in peanut growth, development, and response to environmental stress.

BACKGROUND: Sesame is an important oil crop due to its high oil, antioxidant, and protein content. Drought stress is a major abiotic stress that affects sesame production as well as the quality of sesame seed. To reveal the adaptive mechanism of sesame in response to water deficient conditions, transcriptomic and metabolomics were applied in drought-tolerant (DT) and drought-susceptible (DS) sesame genotypes. RESULTS: Transcriptomic analysis reveals a set of core drought-responsive genes (684 up-regulated and 1346 down-regulated) in sesame that was robustly differently expressed in both genotypes. Most enriched drought-responsive genes are mainly involved in protein processing in endoplasmic reticulum, plant hormone signal transduction photosynthesis, lipid metabolism, and amino acid metabolism. Drought-susceptible genotype was more disturbed by drought stress at both transcriptional and metabolic levels, since more drought-responsive genes/metabolites were identified in DS. Drought-responsive genes associated with stress response, amino acid metabolism, and reactive oxygen species scavenging were more enriched or activated in DT. According to the partial least-squares discriminate analysis, the most important metabolites which were accumulated under drought stress in both genotypes includes ABA, amino acids, and organic acids. Especially, higher levels of ABA, proline, arginine, lysine, aromatic and branched chain amino acids, GABA, saccharopine, 2-aminoadipate, and allantoin were found in DT under stress condition. Combination of transcriptomic and metabolomic analysis highlights the important role of amino acid metabolism (especially saccharopine pathway) and ABA metabolism and signaling pathway for drought tolerance in sesame. CONCLUSION: The results of the present study provide valuable information for better understanding the molecular mechanism underlying drought tolerance of sesame, and also provide useful clues for the genetic improvement of drought tolerance in sesame.

With the impacts of climate change and impending crisis of clean drinking water, designing functional materials for water harvesting from fog with large water capacity has received much attention in recent years. Nature has evolved different strategies for surviving dry, arid, and xeric conditions. Nature is a school for human beings. In this contribution, inspired by the Stenocara beetle, superhydrophilic/superhydrophobic patterned surfaces are fabricated on the silica poly(dimethylsiloxane) (PDMS)‐coated superhydrophobic surfaces using a pulsed laser deposition approach with masks. The resultant samples with patterned wettability demonstrate water‐harvesting efficiency in comparison with the silica PDMS‐coated superhydrophobic surface and the Pt nanoparticles‐coated superhydrophilic surface. The maximum water‐harvesting efficiency can reach about 5.3 g cm −2 h −1 . Both the size and the percentage of the Pt‐coated superhydrophilic square regions on the patterned surface affect the condensation and coalescence of the water droplet, as well as the final water‐harvesting efficiency. The present water‐harvesting strategy should provide an avenue to alleviate the water crisis facing mankind in certain arid regions of the world.

ABSTRACT Knowledge of changes associated with advances in crop productivity is essential for understanding yield limiting factors and developing strategies for future genetic improvement. The objectives of this study are to understand genetic gain for grain yield and associated traits in the Northern China Winter Wheat Region (NCWWR). Four trials, comprised of 47 leading common wheat ( Triticum aestivum L.) cultivars from the NCWWR from 1960 to 2000, were conducted during 2001 to 2003 using a completely randomized block design of three replicates under controlled field environments. Molecular markers were used to detect the presence of dwarfing genes and the 1B/1R translocation. Results showed that average annual genetic gain in grain yield ranged from 32.07 to 72.11 kg ha −1 yr −1 or from 0.48 to 1.23% annually in different provinces. The most significant increase in grain yield occurred in the early 1980s, largely because of the successful utilization of dwarfing genes and the 1B/1R translocation. There was no common trend across trials in terms of changes in spikes m −2 , kernels per spike, 1000‐kernel weight (TKW), or biomass. The genetic improvement in grain yield was primarily attributed to increased grain weight per spike, reduced plant height, and increased harvest index (HI). The dwarfing allele Rht‐D1b was the most frequent (68.0%) among the cultivars, followed by Rht 8 (42.0%) and Rht‐B1b (16.0%). The frequency of 1B/1R translocation cultivars was 42.6%. The future challenge of wheat breeding in this region is to maintain the genetic gain in grain yield and to improve grain quality, without increasing inputs for the wheat‐maize double cropping system.