Occurrence, distribution, potential sources, and risks of organophosphate esters in fresh snow on Urumqi Glacier No. 1, eastern Tien Shan, China.

Organophosphate esters (OPEs), extensively used as flame retardants, are widely detected in various regions and environments. The potential toxicity of OPEs has caused great concern in recent years. Based on the global distillation model, the Tien Shan glaciers, such as Urumqi Glacier No. 1, could be as a potential "sink" for OPEs. However, little is known about the concentration, distribution, potential sources, and ecological risks of OPEs in Tien Shan glaciers. In this study, fresh snow samples were collected at various altitudes on the Urumqi Glacier No. 1, eastern Tien Shan, China. The total concentrations of ten OPEs (Σ10OPEs) ranged from 116 to 152 ng/L. The most abundant OPE was tris-(2-chloroisopropyl) phosphate (TCIPP), contributing to 74 % of the total OPEs. Σ10OPEs, tri-n-butyl phosphate (TnBP), and TCIPP concentrations showed positive correlations with altitude, indicating the effect of cold condensation on OPEs deposition. Based on air mass back-trajectory analysis and principal component analysis, we found that emissions from both traffic and household products in indoor environment were the important sources, and OPEs on the Urumqi Glacier No. 1 might mainly originate from Europe. Our assessment also showed triphenyl phosphate (TPhP) posed a low ecological risk in snow. This is the first systematic study of OPEs on the Tien Shan glaciers.

Abrupt climate fluctuations in Tibet as imprints of multiple meltwater events during the early to mid-Holocene.

Understanding the impact of meltwater discharge during the final stage of the Laurentide Ice Sheet (LIS) has important implications for predicting sea level rise and climate change. Here we present a high-resolution ice-core isotopic record from the central Tibetan Plateau (TP), where the climate is sensitive to the meltwater forcing, and explore possible signals of the climate response to potential LIS meltwater discharges in the early to mid-Holocene. The record shows four abrupt large fluctuations during the 7-9 ka BP (kiloannum before present), reflecting large shifts of the mid-latitude westerlies and the Indian summer monsoon (ISM) over this period, and they corresponded to possible LIS freshwater events documented in other paleoclimate records. Our study suggests that multiple rapid meltwater discharge events might have occurred during the final stage of LIS. The finding implies the possibility of rapid sea level rise and unstable climate in the transition zone between the mid-latitude westerlies and the ISM due to fast polar ice retreat under the anthropogenic global warming.

Genomic characterization and gene bank curation of Aegilops: the wild relatives of wheat.

Genetic diversity found in crop wild relatives is critical to preserve and utilize for crop improvement to achieve sustainable food production amid climate change and increased demand. We genetically characterized a large collection of 1,041 Aegilops accessions distributed among 23 different species using more than 45K single nucleotide polymorphisms identified by genotyping-by-sequencing. The Wheat Genetics Resource Center (WGRC) Aegilops germplasm collection was curated through the identification of misclassified and redundant accessions. There were 49 misclassified and 28 sets of redundant accessions within the four diploid species. The curated germplasm sets now have improved utility for genetic studies and wheat improvement. We constructed a phylogenetic tree and principal component analysis cluster for all Aegilops species together, giving one of the most comprehensive views of Aegilops. The Sitopsis section and the U genome Aegilops clade were further scrutinized with in-depth population analysis. The genetic relatedness among the pair of Aegilops species provided strong evidence for the species evolution, speciation, and diversification. We inferred genome symbols for two species Ae. neglecta and Ae. columnaris based on the sequence read mapping and the presence of segregating loci on the pertinent genomes as well as genetic clustering. The high genetic diversity observed among Aegilops species indicated that the genus could play an even greater role in providing the critical need for untapped genetic diversity for future wheat breeding and improvement. To fully characterize these Aegilops species, there is an urgent need to generate reference assemblies for these wild wheats, especially for the polyploid Aegilops.

Identification and high-resolution mapping of a novel tiller number gene (tin6) by combining forward genetics screen and MutMap approach in bread wheat.

Wheat (Triticum aestivum) is one of the most important food crops worldwide, providing up to 20% of the caloric intake per day. Developing high-yielding wheat cultivars with tolerance against abiotic and biotic stresses is important to keep up with the increasing human population. Tiller number is one of the major yield-related traits, directly affecting the number of grains produced per plant; however, only a small number of QTL and underlining genes have been identified for this important factor. Identification of novel genetic variation underlying contrasting traits and their precise genetic mapping in wheat is considered difficult due to the complexity and size of the genome; however, advancements in genomic resources have made efficient gene localization more possible. In this study, we report the characterization of a novel tillering number gene using a mutant identified in the forward genetic screen of an ethyl methane sulfonate (EMS)-treated population of cv. "Jagger." By crossing the low tillering mutant with the Jagger wild-type plant, we generated an F2 population and used the MutMap approach to identify a novel physical interval on 11 Mb on chromosome 2DS. Using an F2 population of 442 gametes and polymorphic SNP markers, we were able to delineate the tin6 locus to a 2.1 Mb region containing 22 candidate genes.

Wheat doubled haploids have a marked prevalence of chromosomal aberrations.

Double haploid (DH) population development is widely used in many crops, including wheat (Triticum aestivum L.), to rapidly produce fixed germplasm for breeding and genetic studies. The genome shock that takes place during DH induction could induce chromosomal aberrations that can impact genome integrity and subsequently plant fitness and agronomic performance. To evaluate the extent of chromosomal aberrations that exist as a result of the DH process, we studied two wheat DH populations: CDC Stanley×CDC Landmark and KS13H9×SYMonument. We utilized high-throughput skim sequencing to construct digital karyotypes of these populations to quantify deletions and aneuploidy with high resolution and accuracy, which was confirmed in selected plants by cytological analysis. The two populations studied showed high proportion of abnormal primary DH lines, 55 and 45%, respectively, based on at least one abnormality per progeny. The chromosomal abnormalities are genetically unstable and were observed segregating in the subsequent generations. These observations have important implications for the use of DH lines in genetics and breeding.

The wheat stem rust resistance gene Sr43 encodes an unusual protein kinase.

To safeguard bread wheat against pests and diseases, breeders have introduced over 200 resistance genes into its genome, thus nearly doubling the number of designated resistance genes in the wheat gene pool1. Isolating these genes facilitates their fast-tracking in breeding programs and incorporation into polygene stacks for more durable resistance. We cloned the stem rust resistance gene Sr43, which was crossed into bread wheat from the wild grass Thinopyrum elongatum2,3. Sr43 encodes an active protein kinase fused to two domains of unknown function. The gene, which is unique to the Triticeae, appears to have arisen through a gene fusion event 6.7 to 11.6 million years ago. Transgenic expression of Sr43 in wheat conferred high levels of resistance to a wide range of isolates of the pathogen causing stem rust, highlighting the potential value of Sr43 in resistance breeding and engineering.

Exploring genetic diversity of wild and related tetraploid wheat species Triticum turgidum and Triticum timopheevii.

INTRODUCTION: The domestication bottleneck has reduced genetic diversity inwheat, necessitating the use of wild relatives in breeding programs. Wild tetraploid wheat are widely used in the breeding programs but with morphological characters, it is difficult to distinguish these, resulting in misclassification/mislabeling or duplication of accessions in the Gene bank. OBJECTIVES: The study aims to exploreGenotyping by sequencing (GBS) to characterize wild and domesticated tetraploid wheat accessions to generate a core set of accessions to be used in the breeding program. METHODS: TASSEL-GBS pipeline was used for SNP discovery, fastStructure was used to determine the population structure and PowerCore was used to generate a core sets. Nucleotide diversity matrices of Nie's and F-statistics (FST) index were used to determine the center of genetic diversity. RESULTS: We found 65 % and 47 % duplicated accessions in Triticum timopheevii and T. turgidum respectively. Genome-wide nucleotide diversity and FST scan uncovered a lower intra and higher inter-species differentiation. Distinct FST regions were identified in genomic regions belonging to domestication genes: non-brittle rachis (Btr1) and vernalization (VRN-1).Our results suggest that Israel, Jordan, Syria, and Lebanonas the hub of genetic diversity of wild emmer;Turkey, and Georgia for T. durum; and Iraq, Azerbaijan, and Armenia for theT. timopheevii. Identified core set accessions preserved more than 93 % of the available genetic diversity. Genome wide association study (GWAS) indicated the potential chromosomal segment for resistance to leaf rust in T. timopheevii. CONCLUSION: The present study explored the potential of GBS technology in data reduction while maintaining the significant genetic diversity of the species. Wild germplasm showed more differentiation than domesticated accessions, indicating the availability of sufficient diversity for crop improvement. With reduced complexity, the core set preserves the genetic diversity of the gene bank collections and will aid in a more robust characterization of wild germplasm.

A high-throughput skim-sequencing approach for genotyping, dosage estimation and identifying translocations.

The development of next-generation sequencing (NGS) enabled a shift from array-based genotyping to directly sequencing genomic libraries for high-throughput genotyping. Even though whole-genome sequencing was initially too costly for routine analysis in large populations such as breeding or genetic studies, continued advancements in genome sequencing and bioinformatics have provided the opportunity to capitalize on whole-genome information. As new sequencing platforms can routinely provide high-quality sequencing data for sufficient genome coverage to genotype various breeding populations, a limitation comes in the time and cost of library construction when multiplexing a large number of samples. Here we describe a high-throughput whole-genome skim-sequencing (skim-seq) approach that can be utilized for a broad range of genotyping and genomic characterization. Using optimized low-volume Illumina Nextera chemistry, we developed a skim-seq method and combined up to 960 samples in one multiplex library using dual index barcoding. With the dual-index barcoding, the number of samples for multiplexing can be adjusted depending on the amount of data required, and could be extended to 3,072 samples or more. Panels of doubled haploid wheat lines (Triticum aestivum, CDC Stanley x CDC Landmark), wheat-barley (T. aestivum x Hordeum vulgare) and wheat-wheatgrass (Triticum durum x Thinopyrum intermedium) introgression lines as well as known monosomic wheat stocks were genotyped using the skim-seq approach. Bioinformatics pipelines were developed for various applications where sequencing coverage ranged from 1 × down to 0.01 × per sample. Using reference genomes, we detected chromosome dosage, identified aneuploidy, and karyotyped introgression lines from the skim-seq data. Leveraging the recent advancements in genome sequencing, skim-seq provides an effective and low-cost tool for routine genotyping and genetic analysis, which can track and identify introgressions and genomic regions of interest in genetics research and applied breeding programs.

The first detection of organophosphate esters (OPEs) of a high altitude fresh snowfall in the northeastern Tibetan Plateau.

Due to the gradual phase-out of brominated flame retardants, the consumption of organophosphate esters (OPEs) as suitable alternatives has increased in recent years. These compounds could be trapped and accumulate in the widely developed glaciers such as Laohugou Glacier No. 12 in the Tibetan Plateau (TP), as snow is an effective scavenger of organic pollutants in the atmosphere. However, large gaps in knowledge still exist regarding the occurrence, distribution, and source analysis of OPEs in TP glaciers. In this study, eight surface snow samples collected at different altitudes on Laohugou Glacier No. 12 on the northeastern edge of the TP in order to investigate sources and distribution of OPEs. The results showed that the concentrations of ∑7OPEs varied from 54.53 ng/L to 169.15 ng/L, with a mean of 99.84 ng/L. ∑Chlorinated-OPEs (Cl-OPEs) were dominant in these samples, accounting for 83% of the total OPE concentrations. ∑OPEs concentration increases with altitude on Laohugou Glacier No. 12, implying an altitudinal magnification effect on OPEs deposition. Principal component analysis suggests that OPEs primarily originated from traffic emissions and their variations were largely driven by dust transport. Analyses of backward trajectories of air masses and the wind field indicate that these OPEs might have come from urban emissions northwest of Laohugou Glacier No. 12. This study provides the first valuable insight into the environmental behavior of OPEs in Tibetan glaciers.

Temporal variations of the contribution of combustion-derived water vapor to urban humidity during winter in Xi'an, China.

Combustion-derived water vapor (CDV) has significant impacts on urban climate and environment. However, temporal variations of contribution of CDV (CCDV) to urban humidity are unclear due to lack of observations. This study examined the temporal variations of CCDV in Xi'an during winter from 2016 to 2019. We found that the diurnal variation of CCDV is mainly controlled by atmospheric stability, but the peak of CCDV at 9 am is due to the increasing water vapor emission by motor vehicles during the morning rush hour. In addition, the monthly variation of CCDV is related to fossil fuel consumption, but the low values of CCDV in late January and early February is due to substantial decrease of energy utility because of the massive outflow of population during the Spring Festival. Our findings may be helpful for urban pollution control because CDV can play an important role in the secondary conversion of pollutants.

Aegilops sharonensis genome-assisted identification of stem rust resistance gene Sr62.

The wild relatives and progenitors of wheat have been widely used as sources of disease resistance (R) genes. Molecular identification and characterization of these R genes facilitates their manipulation and tracking in breeding programmes. Here, we develop a reference-quality genome assembly of the wild diploid wheat relative Aegilops sharonensis and use positional mapping, mutagenesis, RNA-Seq and transgenesis to identify the stem rust resistance gene Sr62, which has also been transferred to common wheat. This gene encodes a tandem kinase, homologues of which exist across multiple taxa in the plant kingdom. Stable Sr62 transgenic wheat lines show high levels of resistance against diverse isolates of the stem rust pathogen, highlighting the utility of Sr62 for deployment as part of a polygenic stack to maximize the durability of stem rust resistance.

Genetic characterization and curation of diploid A-genome wheat species.

A-genome diploid wheats represent the earliest domesticated and cultivated wheat species in the Fertile Crescent and include the donor of the wheat A sub-genome. The A-genome species encompass the cultivated einkorn (Triticum monococcum L. subsp. monococcum), wild einkorn (T. monococcum L. subsp. aegilopoides (Link) Thell.), and Triticum urartu. We evaluated the collection of 930 accessions in the Wheat Genetics Resource Center (WGRC) using genotyping by sequencing and identified 13,860 curated single-nucleotide polymorphisms. Genomic analysis detected misclassified and genetically identical (>99%) accessions, with most of the identical accessions originating from the same or nearby locations. About 56% (n = 520) of the WGRC A-genome species collections were genetically identical, supporting the need for genomic characterization for effective curation and maintenance of these collections. Population structure analysis confirmed the morphology-based classifications of the accessions and reflected the species geographic distributions. We also showed that T. urartu is the closest A-genome diploid to the A-subgenome in common wheat (Triticum aestivum L.) through phylogenetic analysis. Population analysis within the wild einkorn group showed three genetically distinct clusters, which corresponded with wild einkorn races α, ß, and γ described previously. The T. monococcum genome-wide FST scan identified candidate genomic regions harboring a domestication selection signature at the Non-brittle rachis 1 (Btr1) locus on the short arm of chromosome 3Am at ∼70 Mb. We established an A-genome core set (79 accessions) based on allelic diversity, geographical distribution, and available phenotypic data. The individual species core set maintained at least 79% of allelic variants in the A-genome collection and constituted a valuable genetic resource to improve wheat and domesticated einkorn in breeding programs.

Ice-core based assessment of nitrogen deposition in the central Tibetan Plateau over the last millennium.

Atmospheric nitrogen deposition is a unique source of bioavailable nitrogen for ecosystems in remote regions, and has vital impacts on ecological processes. Understanding variations of atmospheric nitrogen deposition in these regions remains challenging due to a lack of observations. Ice cores contain records of nitrogen species of nitrate (NO3-) and ammonium (NH4+), hence provide valuable long-term data to study past variations of atmospheric nitrogen deposition. In this study, we present an annually resolved record of NH4+ and NO3- over the past millennium, derived from the Zangser Kangri (ZK) ice core in the central Tibetan Plateau. The concentration peaks of NH4+ and NO3- coincide with those of Ca2+ (a dust tracer), indicating that variation of nitrogen species in the ZK ice core is largely driven by dust activities. An EOF analysis for all chemical species (Cl-, SO42-, NO3-, Na+, NH4+, K+, Mg2+, Ca2+) reveals significant but separate loadings of NH4+ and NO3- on EOF 2, suggesting an additional source of nitrogen, likely from biogenic emissions of terrestrial ecosystems. Over the past millennium, the EOF 2 series has relatively high values around 1300 CE and 1600 CE, and has increased significantly since the Industrial Revolution. These variations are likely driven by temperature-dependent biogenic emissions on the Tibetan Plateau. Analyses of seasonal air mass backward trajectories and wind fields find that the chemical concentrations in the ZK ice core are mostly influenced by the westerly, but South Asia summer monsoon plays an important role in the transport of nitrogen species generated from biogenic emissions. This is further confirmed by the significant correlation between EOF 2 series and the South Asian summer monsoon index. This study provides new insight into the preindustrial sources, natural variabilities and major drivers of nitrogen deposition on the Tibetan Plateau.

Population genomic analysis of Aegilops tauschii identifies targets for bread wheat improvement.

Aegilops tauschii, the diploid wild progenitor of the D subgenome of bread wheat, is a reservoir of genetic diversity for improving bread wheat performance and environmental resilience. Here we sequenced 242 Ae. tauschii accessions and compared them to the wheat D subgenome to characterize genomic diversity. We found that a rare lineage of Ae. tauschii geographically restricted to present-day Georgia contributed to the wheat D subgenome in the independent hybridizations that gave rise to modern bread wheat. Through k-mer-based association mapping, we identified discrete genomic regions with candidate genes for disease and pest resistance and demonstrated their functional transfer into wheat by transgenesis and wide crossing, including the generation of a library of hexaploids incorporating diverse Ae. tauschii genomes. Exploiting the genomic diversity of the Ae. tauschii ancestral diploid genome permits rapid trait discovery and functional genetic validation in a hexaploid background amenable to breeding.

Assessment of heavy metal contamination in the atmospheric deposition during 1950-2016 A.D. from a snow pit at Dome A, East Antarctica.

Antarctic trace element records could provide important insights into the impact of human activities on the environment over the past few centuries. In this study, we investigated the atmospheric concentrations of 14 representative heavy metals (Al, As, Cd, Co, Cu, Fe, K, Mg, Mn, Pb, Sb, Sr, Tl and V) from 174 samples collected in a 4-m snow pit at Dome Argus (Dome A) on the East Antarctic Plateau, covering the period from 1950 to 2016 A.D. We found great variability in the annual concentration of all metals. The crustal enrichment factors suggest that the concentrations of some heavy metals (Cd, Sb, Cu, As and Pb) were likely influenced by anthropogenic activities in recent decades. An analysis of source regions suggests that heavy metal pollution at Dome A was largely caused by human activities in Australia and South America (e.g. mining production, leaded gasoline). Based on the relationship between the trace elements fluxes and sea ice concentration (SIC), sea surface temperature (SST) and annual mean air temperature at 2 m above the ground (T2m), our analysis shows that deposition and transport of atmospheric aerosol at Dome A were influenced by circum-Antarctic atmospheric circulations.

Daily precipitation isotope variation in Midwestern United States: Implication for hydroclimate and moisture source.

Stable isotopes of oxygen (δ18O) and hydrogen (δD) in precipitation can be used as dual conservative tracers in the hydrologic cycle and help to understand hydrological and atmospheric processes. Although long-term monthly precipitation global isotope datasets are available in some locations, currently there are limited daily precipitation isotope data, particularly in the Midwest region of the USA. In this study we report a daily precipitation δ18O and δD dataset from March 2014-December 2017 in Dayton, Ohio, the USA. The daily δ18O and δD vary from -28.0 to 0.4‰, and -214.0 to 9.0‰ respectively. The data exhibit strong seasonality with lower δ18O and δD values in the winter and higher values in the summer. The precipitation isotopic values are mainly controlled by temperature, and show no correlation with precipitation amount and relative humidity. However, δ18O-temperature relationship varies among different seasons. The correlation is the strongest in winter (R2 = 0.56), weaker in spring (R2 = 0.28) and fall (R2 = 0.24), and almost non-existent in summer (R2 = 0.1). The slope values also vary with highest value in winter (0.68‰/OC) and much smaller in other seasons. The HYSPLIT back trajectory analyses show that Pacific, Gulf of Mexico, Arctic and Continental moistures are the main sources for southwestern Ohio with different seasonal contributions. The isotopic compositions of precipitation from different sources show small intra-season variations but large seasonal variability. Our daily-resolved dataset provides new insights into the main controls on the isotopic composition of precipitation and its seasonal variations, which could help to understand atmospheric processes and enable their proper use in interpretation of paleoclimate proxies, particularly those with seasonal bias.

Genomic Analysis Confirms Population Structure and Identifies Inter-Lineage Hybrids in Aegilops tauschii.

Aegilops tauschii, the D-genome donor of bread wheat, Triticum aestivum, is a storehouse of genetic diversity, and an important resource for future wheat improvement. Genomic and population analysis of 549 Ae. tauschii and 103 wheat accessions was performed by using 13,135 high quality SNPs. Population structure, principal component, and cluster analysis confirmed the differentiation of Ae. tauschii into two lineages; lineage 1 (L1) and lineage 2 (L2), the latter being the wheat D-genome donor. Lineage L1 contributes only 2.7% of the total introgression from Ae. tauschii for a set of United States winter wheat lines, confirming the great amount of untapped genetic diversity in L1. Lineage L2 accessions had overall greater allelic diversity and wheat accessions had the least allelic diversity. Both lineages also showed intra-lineage differentiation with L1 being driven by longitudinal gradient and L2 differentiated by altitude. There has previously been little reported on natural hybridization between L1 and L2. We found nine putative inter-lineage hybrids in the population structure analysis, each containing numerous lineage-specific private alleles from both lineages. One hybrid was confirmed as a recombinant inbred between the two lineages, likely artificially post collection. Of the remaining eight putative hybrids, a group of seven from Georgia carry 713 SNPs with private alleles, which points to the possibility of a novel L1-L2 hybrid lineage. To facilitate the use of Ae. tauschii in wheat improvement, a MiniCore consisting of 29 L1 and 11 L2 accessions, has been developed based on genotypic, phenotypic and geographical data. MiniCore reduces the collection size by over 10-fold and captures 84% of the total allelic diversity in the whole collection.

Efficient curation of genebanks using next generation sequencing reveals substantial duplication of germplasm accessions.

Genebanks are valuable resources for crop improvement through the acquisition, ex-situ conservation and sharing of unique germplasm among plant breeders and geneticists. With over seven million existing accessions and increasing storage demands and costs, genebanks need efficient characterization and curation to make them more accessible and usable and to reduce operating costs, so that the crop improvement community can most effectively leverage this vast resource of untapped novel genetic diversity. However, the sharing and inconsistent documentation of germplasm often results in unintentionally duplicated collections with poor characterization and many identical accessions that can be hard or impossible to identify without passport information and unmatched accession identifiers. Here we demonstrate the use of genotypic information from these accessions using a cost-effective next generation sequencing platform to find and remove duplications. We identify and characterize over 50% duplicated accessions both within and across genebank collections of Aegilops tauschii, an important wild relative of wheat and source of genetic diversity for wheat improvement. We present a pipeline to identify and remove identical accessions within and among genebanks and curate globally unique accessions. We also show how this approach can also be applied to future collection efforts to avoid the accumulation of identical material. When coordinated across global genebanks, this approach will ultimately allow for cost effective and efficient management of germplasm and better stewarding of these valuable resources.

Corrigendum: Possible recent warming hiatus on the northwestern Tibetan Plateau derived from ice core records.

This corrects the article DOI: 10.1038/srep32813.