Astragalusliuaiminii, a new species of Astragalus (Fabaceae) from Xinjiang, China.

A new species, Astragalusliuaiminii Z. Z. Yang & Q. R. Liu (Fabaceae), is described and illustrated from Xinjiang Province, China. The new species is close to A.wenquanensis S. B. Ho, but differs from the latter by leaves having a single leaflet (vs. 3-5 leaflets), and inflorescences with 1-2 flowers (vs. inflorescences with 5-7 flowers). It is also similar to A.monophyllus Maxim in leaf shape, but differs by its calyx expanding to become saccate and totally enveloping the pod (vs. calyx tubular, and ruptured by pod after flowering).

Cytology, metabolomics, and proteomics reveal the grain filling process and quality difference of wheat.

Comparative proteomics and non-target metabolomics, together with physiological and microstructural analyses of wheat grains (at 15, 20, 25, and 30 days after anthesis) from two different quality wheat varieties (Gaoyou 5766 (strong-gluten) and Zhoumai 18) were performed to illustrate the grain filling material dynamics and to search for quality control genes. The differential expressions of 1541 proteins and 406 metabolites were found. They were mostly engaged in protein metabolism, stress/defense, energy metabolism, and amino acid metabolism, and the metabolism of stored proteins and carbohydrates was the major focus of the latter stages. The core proteins and metabolites in the growth process were identified, and the candidate genes for quality differences were screened. In conclusion, this study offers a molecular explanation for the establishment of wheat quality, and it aids in our understanding of the intricate metabolic network between different qualities of wheat at the filling stage.

The wheat WRKY transcription factor TaWRKY1-2D confers drought resistance in transgenic Arabidopsis and wheat (Triticum aestivum L.).

The WRKY transcription factor family has been associated with a variety of plant biological processes, such as biotic and abiotic stress responses. In this study, 13 wheat TaWRKY DEGs in transcriptome data before and after drought stress, namely TaWRKY1 to TaWRKY8, including various copies, were identified and classified as Group I, II, or III. TaWRKY1-2D overexpression enhanced drought tolerance in transgenic Arabidopsis. Moreover, the AtRD29A, AtP5CS1, AtPOD1, AtCAT1, and AtSOD (Cu/Zn) genes, which are related to the stress response and antioxidant system, were significantly upregulated in TaWRKY1-2D transgenic Arabidopsis under drought stress. TaWRKY1-2 silencing in wheat increases the MDA content, reduces the contents of proline and chlorophyll and the activities of antioxidant enzymes, and inhibits the expression levels of antioxidant (TaPOD, TaCAT, and TaSOD (Fe))- and stress-related genes (TaP5CS) under drought stress. Yeast two-hybrid screening revealed TaDHN3 as an interaction partner of TaWRKY1-2D; their interaction was further confirmed using yeast two-hybrid and bimolecular fluorescence complementation. Furthermore, TaWRKY1-2D may play essential roles in wheat drought tolerance through posttranslational regulation of TaDHN3. Overall, these findings contribute to our knowledge of the WRKY family in wheat and identify TaWRKY1-2D as a promising candidate gene for improving wheat breeding to generate drought-tolerant wheat.

Chromosome-level genome assembly of the Siberian chipmunk (Tamias sibiricus).

Tamias sibiricus is regarded as one predominant scatter-hoarder that stores their food items both in small scattered caches and underground larder-hoards. This unique behavior, though providing essential seed dispersal services for many plant species worldwide, relies highly on accurate spatial memory and acute sense of olfaction. Here, we assembled a chromosome-scale genome of T. sibiricus using Illumina sequencing, PacBio sequencing and chromosome structure capture technique. The genome was 2.64 Gb in size with scaffold N50 length of 172.61 Mb. A total of 2.59 Gb genome data was anchored and orientated onto 19 chromosomes (ranging from 28.70 to 222.90 Mb) with a mounting rate of up to 98.03%. Meanwhile, 25,311 protein-coding genes were predicted with an average gene length of 32,936 bp, and 94.73% of these genes were functionally annotated. This reference genome will be a valuable resource for in-depth studies on basic biological possess and environmental adaptation of the Siberian chipmunk, as well as promoting comparative genomic analyses with other species within Rodentia.

Genome-wide identification of foxtail millet's TRX family and a functional analysis of SiNRX1 in response to drought and salt stresses in transgenic Arabidopsis.

Thioredoxins (TRXs) are small-molecule proteins with redox activity that play very important roles in the growth, development, and stress resistance of plants. Foxtail millet (Setaria italica) gradually became a model crop for stress resistance research because of its advantages such as its resistance to sterility and its small genome. To date, the thioredoxin (TRX) family has been identified in Arabidopsis thaliana, rice and wheat. However, studies of the TRX family in foxtail millet have not been reported, and the biological function of this family remains unclear. In this study, 35 SiTRX genes were identified in the whole genome of foxtail millet through bioinformatic analysis. According to phylogenetic analysis, 35 SiTRXs can be divided into 13 types. The chromosome distribution, gene structure, cis-elements and conserved protein motifs of 35 SiTRXs were characterized. Three nucleoredoxin (NRX) members were further identified by a structural analysis of TRX family members. The expression patterns of foxtail millet's SiNRX members under abiotic stresses showed that they have different stress-response patterns. In addition, subcellular localization revealed that SiNRXs were localized to the nucleus, cytoplasm and membrane. Further studies demonstrated that the overexpression of SiNRX1 enhanced Arabidopsis' tolerance to drought and salt stresses, resulting in a higher survival rate and better growth performance. Moreover, the expression levels of several known stress-related genes were generally higher in overexpressed lines than in the wild-type. Thus, this study provides a general picture of the TRX family in foxtail millet and lay a foundation for further research on the mechanism of the action of TRX proteins on abiotic stresses.

Identification of TaBADH-A1 allele for improving drought resistance and salt tolerance in wheat (Triticum aestivum L.).

Drought and salt stress can strongly affect the growth and development of wheat. Wheat adapts to drought and salt stress through osmotic regulation. Betaine aldehyde dehydrogenase (BADH) is a key enzyme in the synthesis of betaine, an osmotic regulator. We cloned a region of the TaBADH-A1 promoter and genomic DNA that included the introns and exons, from four Chinese wheat cultivars. Following the analysis of TaBADH-A1 genomic DNA and promoter sequence polymorphisms of 4 cloned and 15 cultivars from the database, 7 haplotypes of TaBADH-A1 gene were identified. We divided the 7 haplotypes with a 254 bp insertion or deletion (indel) into two main alleles, BADH-A1a and BADH-A1b. Meanwhile, a molecular marker was developed based on the 254 bp indel of the third intron of TaBADH-A1 gene. Expression levels of BADH-A1b were found to be significantly higher than those of BADH-A1a under drought and salt stress conditions. Betaine accumulation was significantly higher in wheat containing BADH-A1b compared to BADH-A1a under drought and salt stress. We also identified that the average relative germination and survival rates of wheat with the BADH-A1b allele were significantly higher than wheat with the BADH-A1a allele. The results reveal that wheat containing BADH-A1b has stronger drought and salt tolerance than wheat with BADH-A1a. Meanwhile, the geographic distribution and frequency of the TaBADH-A1 locus alleles indicate that BADH-A1a has been preferred in Chinese wheat breeding programs, while BADH-A1b, associated with favorable stress tolerance, has been neglected. The results of this study provide evidence for an excellent candidate allele for marker-assisted selection of new wheat cultivars with increased salt tolerance and drought resistance.

Genome-wide Association Study for Starch Pasting Properties in Chinese Spring Wheat.

In order to understand the genetic basis of starch pasting viscosity characteristics of Chinese spring wheat, we assessed the genetic variation of RVA parameters determined by the Rapid Visco Analyser in a panel of 192 Chinese spring wheat accessions grown in Er'shi, Shihezi and Zhaosu during 2012 and 2013 cropping seasons. A genome-wide association study with 47,362 single nucleotide polymorphism (SNP) markers was conducted to detect marker-trait associations using mixed linear model. Phenotypic variations of RVA parameters ranged from 1.6 to 30.7% and broad-sense heritabilities ranged from 0.62 to 0.91. Forty-one SNP markers at 25 loci were significantly associated with seven RVA traits in at least two environments; among these, 20 SNPs were located in coding sequences (CDS) of 18 annotation genes, which can lead to discovering novel genes underpinning starch gelatinization in spring wheat. Haplotype analysis revealed one block for breakdown (BD) on chromosome 3B and two blocks for pasting temperature (T) on chromosome 7B. Cultivars with superior haplotypes at these loci showed better starch pasting viscosity than the average of all cultivars surveyed. The identified loci and associated markers provide valuable sources for future functional characterization and genetic improvement of starch quality in wheat.

Transcriptomic Identification of Wheat AP2/ERF Transcription Factors and Functional Characterization of TaERF-6-3A in Response to Drought and Salinity Stresses.

AP2/ERF (APETALA2/ethylene responsive factor) is a family of plant-specific transcription factors whose members are widely involved in many biological processes, such as growth, development, and biotic and abiotic stress responses. Here, 20 AP2/ERF genes were identified based on wheat RNA-seq data before and after drought stress, and classified as AP2, ERF, DREB, and RAV. The analysis of gene structure revealed that about 85% of AP2/ERF family members had lost introns, which are presumed to have been lost during the formation and evolution of the wheat genome. The expression of 20 AP2/ERF family genes could be verified by qRT-PCR, which further supported the validity of the RNA-seq data. Subsequently, subcellular localization and transcriptional activity experiments showed that the ERF proteins were mainly located in the nucleus and were self-activating, which further supports their functions as transcription factors. Furthermore, we isolated a novel ERF gene induced by drought, salt, and cold stresses and named it TaERF-6-3A. TaERF-6-3A overexpression increased sensitivity to drought and salt stresses in Arabidopsis, which was supported by physiological and biochemical indices. Moreover, the expression of stress- and antioxidant-related genes was downregulated in TaERF-6-3A-overexpressing plants. Overall, these results contribute to the further understanding of the TaERF-6-3A gene function in wheat.

Genome-wide identification, characterization, evolution, and expression pattern analyses of the typical thioredoxin gene family in wheat (Triticum aestivum L.).

Typical thioredoxin (TRX) plays an important role in maintaining redox balance in plants. However, the typical TRX genes in wheat still need to be comprehensively and deeply studied. In this research, a total of 48 typical TaTRX genes belonging to eight subtypes were identified via a genome-wide search in wheat, and the gene structures, protein conserved motifs, and protein 3D structures of the same subtype were very similar. Evolutionary analysis showed that there are two pairs of tandem duplication genes and 14 clusters of segmental duplication genes in typical TaTRX family members; TaTRX15, TaTRX36, and TaTRX42 had positive selection compared with the orthologs of their ancestral species; rice and maize have 11 and 13 orthologous typical TRXs with wheat, respectively. Gene Ontology (GO) analysis indicated that typical TaTRXs were involved in maintaining redox homeostasis in wheat cells. Estimation of ROS content, determination of antioxidant enzyme activity, and gene expression analysis in a line overexpressing one typical TaTRX confirmed that TRX plays an important role in maintaining redox balance in wheat. A predictive analysis of cis-acting elements in the promoter region showed that typical TaTRXs were extensively involved in various hormone metabolism and response processes to stress. The results predicted using public databases or verified using RT-qPCR show that typical TaTRXs were able to respond to biotic and abiotic stresses, and their expression in wheat was spatiotemporal. A total of 16 wheat proteins belonging to four different families interacting with typical TaTRXs were predicted. The above comprehensive analysis of typical TaTRX genes can enrich our understanding of this gene family in wheat and provide valuable insights for further gene function research.

The role of AUX1 during lateral root development in the domestication of the model C4 grass Setaria italica.

C4 photosynthesis increases the efficiency of carbon fixation by spatially separating high concentrations of molecular oxygen from Rubisco. The specialized leaf anatomy required for this separation evolved independently many times. The morphology of C4 root systems is also distinctive and adapted to support high rates of photosynthesis; however, little is known about the molecular mechanisms that have driven the evolution of C4 root system architecture. Using a mutant screen in the C4 model plant Setaria italica, we identify Siaux1-1 and Siaux1-2 as root system architecture mutants. Unlike in S. viridis, AUX1 promotes lateral root development in S. italica. A cell by cell analysis of the Siaux1-1 root apical meristem revealed changes in the distribution of cell volumes in all cell layers and a dependence of the frequency of protophloem and protoxylem strands on SiAUX1. We explore the molecular basis of the role of SiAUX1 in seedling development using an RNAseq analysis of wild-type and Siaux1-1 plants and present novel targets for SiAUX1-dependent gene regulation. Using a selection sweep and haplotype analysis of SiAUX1, we show that Hap-2412TT in the promoter region of SiAUX1 is an allele which is associated with lateral root number and has been strongly selected for during Setaria domestication.

A Wheat TaTOE1-B1 Transcript TaTOE1-B1-3 Can Delay the Flowering Time of Transgenic Arabidopsis.

Flowering time is one of the most important agronomic traits in wheat production. A proper flowering time might contribute to the reduction or avoidance of biotic and abiotic stresses, adjust plant architecture, and affect the yield and quality of grain. In this study, TaTOE1-B1 in wheat produced three transcripts (TaTOE1-B1-1, TaTOE1-B1-2, and TaTOE1-B1-3) by alternative splicing. Compared to the longest transcript, TaTOE1-B1-1, TaTOE1-B1-3 has a deletion in the sixth exon (1219-1264 bp). Under long-day conditions, the heterologous overexpression of the TaTOE1-B1-3 gene delayed flowering, prolonged the vegetative growth time, and enlarged the vegetative body of Arabidopsis, but that of TaTOE1-B1-1 did not. As typical AP2 family members, TaTOE1-B1-1 and TaTOE1-B1-3 are mainly located in the nucleus and have transcriptional activation activities; the transcriptional activation region of TaTOE1-B1-3 is located in the C-terminal. In TaTOE1-B1-3 overexpression lines, the expression of flowering-related AtFT and AtSOC1 genes is significantly downregulated. In addition, this study confirms the protein-protein interaction between TaTOE1-B1-3 and TaPIFI, which may play an important role in flowering inhibition. These results provide a theoretical basis for the precise regulation of wheat flowering time.

Identification of a 193 bp promoter region of TaNRX1-D gene from common wheat that contributes to osmotic or ABA stress inducibility in transgenic Arabidopsis.

BACKGROUND: Cloning and characterizing the drought-inducible promoters is essential for their use in crop resistance's genetic improvement. Previous studies have shown that the TaNRX1-D gene participates in regulating the response of wheat to drought stress. However, its promoter has not yet been identified. OBJECTIVE: In this study, we aimed to characterize the promoter of the TaNRX1-D gene. METHODS: The promoter of TaNRX1-D (named P0, 2081 bp) was isolated from common wheat with several cis-acting elements that regulate in response to abiotic stresses and some core cis-acting elements. Functional verification of the promoter, eight 5'-deletion fragments of TaNRX1-D promoter, was fused to the ß-glucuronidase (GUS) gene P0::GUS ~ P7::GUS and transformed into Arabidopsis, respectively. Agrobacterium-mediated GUS transient assay the P6a and P6b promoter regions in tobacco leaves under normal, osmotic or ABA stress. RESULTS: Activity analysis of the full-length promoter (P0) showed that the intensity of stronger ß-glucuronidase (GUS) staining in the roots and leaves was obtained during the growth of transgenic Arabidopsis. P0::GUS displayed the GUS activity was much higher in the roots and leaves than in other parts of the transgenic plant under normal conditions, which was similarly within wheat. Analysis of the 5'-deletion fragments revealed that P0::GUS ~ P6::GUS responded well upon exposure to osmotic (polyethylene glycol-6000, PEG6000) and abscisic acid (ABA) stress treatments and expressed significantly higher GUS activity than the CaMV35S promoter (35S::GUS), while P7::GUS did not. GUS transient assay in tobacco leaves showed that the GUS activities of P6a and P6b were lower than P6 in the PEG6000 and ABA stresses. CONCLUSION: The 193 bp (P6) segment was considered the core region of TaNRX1-D responding to PEG6000 or ABA treatment. GUS activity assay in transgenic Arabidopsis showed that this segment was sufficient for the PEG6000 or ABA stress response. The identified 193 bp promoter of TaNRX1-D in this study will help breed osmotic or ABA tolerant crops. The 36 bp segment between P6 and P6b (-193 to -157 bp) was considered the critical sequence for the TaNRX1-D gene responding to PEG6000 or ABA treatment.

One acorn produces two seedlings in Chinese cork oak Quercus variabilis.

Although the early germination of white oaks has long been considered an adaptation to counter animal predation, the role of the robust radicles of white oak acorns has been largely neglected in the interaction between acorns and seed-eating animals. Here, the regeneration capabilities of the pruned radicles of intermediate oak Quercus variabilis left by the acorn-eating animals were compared to test the 'one acorn produce two seedlings' hypothesis stating that the remnant radicles exhibit the capability to produce normal seedlings owning to their atypical nutritional and anatomical characteristics. Our results first showed that both pruned radicle and cotyledons from single acorn successfully established seedlings, providing strong evidence on an old puzzle that the robust radicles of early-germinating oak acorns act as reserved propagules, allowing them to escape animals' predation. Our study also suggests that much of the investment in the food reserves of an acorn may be important as a food reward for the animals that disperse the acorns, rather than simply serving as energy for the young seedling.

Loose Panicle1 encoding a novel WRKY transcription factor, regulates panicle development, stem elongation, and seed size in foxtail millet [Setaria italica (L.) P. Beauv.].

Panicle development is an important agronomic trait that aids in determining crop productivity. Foxtail millet and its wild ancestor green foxtail have recently been used as model systems to dissect gene functions. Here, we characterized a recessive mutant of foxtail millet, loose-panicle 1 (lp1), which showed pleiotropic phenotypes, such as a lax primary branching pattern, aberrant branch morphology, semi-dwarfism, and enlarged seed size. The loose panicle phenotype was attributed to increased panicle lengths and decreased primary branch numbers. Map-based cloning, combined with high-throughput sequencing, revealed that LP1, which encodes a novel WRKY transcription factor, is responsible for the mutant phenotype. A phylogenetic analysis revealed that LP1 belongs to the Group I WRKY subfamily, which possesses two WRKY domains (WRKY I and II). A single G-to-A transition in the fifth intron of LP1 resulted in three disorganized splicing events in mutant plants. For each of these aberrant splice variants, the normal C2H2 motif in the WRKY II domain was completely disrupted, resulting in a loss-of-function mutation. LP1 mRNA was expressed in all of the tissues examined, with higher expression levels observed in inflorescences, roots, and seeds at the grain-filling stage. A subcellular localization analysis showed that LP1 predominantly accumulated in the nucleus, which confirmed its role as a transcriptional regulator. This study provides novel insights into the roles of WRKY proteins in regulating reproductive organ development in plants and may help to develop molecular markers associated with crop yields.

Analysis of chromosomal structural polymorphisms in the St, P, and Y genomes of Triticeae (Poaceae).

The St, P, and Y genomes are three important genomes in the tribe Triticeae, which includes many perennial species. To study polymorphisms within the chromosomes of the St, P, and Y genomes, a GISH-FISH method was developed that allowed them to be clearly distinguished. The karyotypes of five individuals from population Z1925 of Kengyilia grandiglumis (Keng) J.L. Yang et al. (2n = 6x = 42, StStPPYY) were analyzed. The results showed that there were structural polymorphisms in all of the chromosomes from the three individual genomes. The polymorphisms were found mainly in the terminal regions of chromosomes and infrequently near the centromeric region. Of all the chromosomes, 1P, 1St, 1Y, 2Y, 3St, and 3Y showed the most polymorphisms. The polymorphisms within the individual chromosomes suggested that more extensive and scientific conclusions regarding the origin and evolution of genomes in wild species of Triticeae would be achieved by studying a population as a sampling and analysis unit.