Investigation of the Petrological and Geochemical Characteristics of Siderite in the Early Cretaceous Sandstone of Lacustrine Sedimentary Sequence in the Erlian Basin from Northeastern China

Siderite is a prevalent authigenic mineral in siliciclastic rocks, which usually occurred in eodiagensis period and could be used as an indicator of sedimentary environment. Some siderite precipitated in burial depth with geochemical information of basin fluid evolution. The crystal morphology, geochemical composition, and isotope values are influenced by physical and geochemical environment of precipitation. In this study, samples from the Early Cretaceous of Erlian basin in the northwestern China were collected, and mineralogy, bulk and in-situ geochemistry, C and O isotopes were analyzed to comprehensively investigate the sedimentary and diagenetic environment that the sediments experienced. Six lithofaices with three types of crystal habits were recognized in the siderite-rich sandstone, bundle crystal in spherical forms, blocky rhombs in intergranular pore and cleavage of muscovite, and micro bundle and mosaic crystals aggregates in nodular. The siderite growth proceeds through micro bundle and mosaic crystals to bundle siderite aggregates and then into blocky rhombs. The crystal evolution is also reflected by geochemical composition. The micro bundle and mosaic crystals are Casiderite. The spheritic shaped bundle aggregates are Ca-Mn-siderite. The blocky rhomb siderite shows gray part and bight part with Ca, Mg and Mn varies. Increase of Ca in block rhomb siderite suggests burial and mesodiagenesis, the high content of Mn may have linkage with eogenetic effects. The relatively positive and slightly negative δ13C value indicates meteoric water domination and influence of organic matter evolution in shallow buried time. The narrow ranges negative δ18O value suggest a small span of temperature of siderite formation.

Engineered Cleistogamy in Camelina sativa for bioconfinement

Camelina sativa is a self-pollinating and facultative outcrossing oilseed crop.Genetic engineering has been used to improve camelina yield potential for altered fatty acid composition,modified protein profiles,improved seed and oil yield,and enhanced drought resistance.The deployment of transgenic camelina in the field posits high risks related to the introgression of transgenes into nontransgenic camelina and wild relatives.Thus,effective bioconfinement strategies need to be developed to prevent pollen-mediated gene f low(PMGF)from transgenic camelina.In the present study,we overexpressed the cleistogamy(i.e.f loral petal non-openness)-inducing PpJAZ1 gene from peach in transgenic camelina.Transgenic camelina overexpressing PpJAZ1 showed three levels of cleistogamy,affected pollen germination rates after anthesis but not during anthesis,and caused a minor silicle abortion only on the main branches.We also conducted field trials to examine the effects of the overexpressed PpJAZ1 on PMGF in the field,and found that the overexpressed PpJAZ1 dramatically inhibited PMGF from transgenic camelina to non-transgenic camelina under the field conditions.Thus,the engineered cleistogamy using the overexpressed PpJAZ1 is a highly effective bioconfinement strategy to limit PMGF from transgenic camelina,and could be used for bioconfinement in other dicot species.

An optimized protocol for stepwise optimization of real-time RT-PCR analysis

Computational tool-assisted primer design for real-time reverse transcription(RT)PCR(qPCR)analysis largely ignores the sequence similarities between sequences of homologous genes in a plant genome.It can lead to false confidence in the quality of the designed primers,which sometimes results in skipping the optimization steps for qPCR.However,the optimization of qPCR parameters plays an essential role in the efficiency,specificity,and sensitivity of each gene’s primers.Here,we proposed an optimized approach to sequentially optimizing primer sequences,annealing temperatures,primer concentrations,and cDNA concentration range for each reference(and target)gene.Our approach started with a sequence-specific primer design that should be based on the single-nucleotide polymorphisms(SNPs)present in all the homologous sequences for each of the reference(and target)genes under study.By combining the efficiency calibrated and standard curve methods with the 2−ΔΔCt method,the standard cDNA concentration curve with a logarithmic scale was obtained for each primer pair for each gene.As a result,an R 2≥0.9999 and the efficiency(E)=100±5% should be achieved for the best primer pair of each gene,which serve as the prerequisite for using the 2^(−ΔΔCt) method for data analysis.We applied our newly developed approach to identify the best reference genes in different tissues and at various inflorescence developmental stages of Tripidium ravennae,an ornamental and biomass grass,and validated their utility under varying abiotic stress conditions.We also applied this approach to test the expression stability of six reference genes in soybean under biotic stress treatment with Xanthomonas axonopodis pv.glycines(Xag).Thus,these case studies demonstrated the effectiveness of our optimized protocol for qPCR analysis.

New opportunities for using WUS/BBM and GRF-GIF genes to enhance genetic transformation of ornamental plants

Broad application of plant transformation remains challenging because the efficiency of plant regeneration and regeneration-based transformation in many plant species is extremely low.Many species and genotypes are not responsive to traditional hormone-based regeneration systems.This regeneration recalcitrance hampers the application of many technologies such as micropropagation,transgenic breeding,and gene editing in various plant species,including ornamental flowers,shrubs,and trees.Various developmental genes have long been studied for their ability to improve plant meristematic induction and regeneration.Lately,it was demonstrated that the combined and refined expression of morphogenic regulator genes WUSCHEL and BABY BOOM could alleviate their pleiotropic effects and permit transformation in recalcitrant monocots.Moreover,ectopic expression of plant growth-regulating factors(GRFs)alone or in combination with GRF-interacting factors(GIFs)improved the regeneration and transformation of dicot and monocot species.Fine-tuning the expression of these genes provides new opportunities to improve transformation efficiencies and facilitate the application of new breeding technologies in ornamental plants.

Exploring Sandstone Body in Weak Electrical Resistivity Contrast with AMT Data

AMT method with the economical and convenient superiority plays a key role in exploring the sandstone-type uranium deposits in China, which mainly meets to four problems such as the thickness of overlying strata, delineating the shape of the significant sand bodies, whether there are buried structures and knowing the basement relief. Exploring the sand body shape is the key one among such problems because sand body provides the room of uranium deposits and is the prerequisite for exploring uranium mineralization. Through an example of outlining the sandstone layer within the mudstone layers, the ability can be improved to recognize the electrical resistivity anomaly among the weak electrical property contrast by adjusting the inversion model’s scale. A route to deal with the problem was given by inverting different scale models followed by checking whether the anomalies of each inversion are reliable. Finally, the geo-electrical model was to be determined by comparing results of different scale model.

Differential SW16.1 allelic effects and genetic backgrounds contributed to increased seed weight after soybean domestication

Although seed weight has increased following domestication from wild soybean(Glycine soja) to cultivated soybean(Glycine max), the genetic basis underlying this change is unclear. Using mapping populations derived from chromosome segment substitution lines of wild soybean, we identified SW16.1 as the causative gene underlying a major quantitative trait locus controlling seed weight.SW16.1 encodes a nucleus-localized LIM domaincontaining protein. Importantly, the GsSW16.1 allele from wild soybean accession N24852 had a negative effect on seed weight, whereas the GmSW16.1 allele from cultivar NN1138-2 had a positive effect. Gene expression network analysis,reverse-transcription quantitative polymerase chain reaction, and promoter-luciferase reporter transient expression assays suggested that SW16.1 regulates the transcription of MT4, a positive regulator of seed weight. The natural variations in SW16.1 and other known seed weight genes were analyzed in soybean germplasm. The SW16.1 polymorphism was associated with seed weight in 247 soybean accessions, showing much higher frequency of positive-effect alleles in cultivated soybean than in wild soybean. Interestingly,gene allele matrix analysis of the known seed weight genes revealed that G. max has lost 38.5%of the G. soja alleles and that most of the lost alleles had negative effects on seed weight. Our results suggest that eliminating negative alleles from G. soja led to a higher frequency of positive alleles and changed genetic backgrounds in G. max,which contributed to larger seeds in cultivated soybean after domestication from wild soybean.Our findings provide new insights regarding soybean domestication and should assist current soybean breeding programs.

Plant Promoters and Terminators for High-Precision Bioengineering

High-precision bioengineering and synthetic biology require fine-tuning gene expression at both transcriptional and posttranscriptional levels.Gene transcription is tightly regulated by promoters and terminators.Promoters determine the timing,tissues and cells,and levels of the expression of genes.Terminators mediate transcription termination of genes and affect mRNA levels posttranscriptionally,e.g.,the 3′-end processing,stability,translation efficiency,and nuclear to cytoplasmic export of mRNAs.The promoter and terminator combination affects gene expression.In the present article,we review the function and features of plant core promoters,proximal and distal promoters,and terminators,and their effects on and benchmarking strategies for regulating gene expression.

The genomic and bulked segregant analysis of Curcuma alismatifolia revealed its diverse bract pigmentation

Compared with most flowers where the showy part comprises specialized leaves(petals)directly subtending the reproductive structures,most Zingiberaceae species produce showy“flowers”through modifications of leaves(bracts)subtending the true flowers throughout an inflorescence.Curcuma alismatifolia,belonging to the Zingiberaceae family,a plant species originating from Southeast Asia,has become increasingly popular in the flower market worldwide because of its varied and esthetically pleasing bracts produced in different cultivars.Here,we present the chromosome-scale genome assembly of C.alismatifolia“Chiang Mai Pink”and explore the underlying mechanisms of bract pigmentation.Comparative genomic analysis revealed C.alismatifolia contains a residual signal of whole-genome duplication.Duplicated genes,including pigment-related genes,exhibit functional and structural differentiation resulting in diverse bract colors among C.alismatifolia cultivars.In addition,we identified the key genes that produce different colored bracts in C.alismatifolia,such as F3′5'H,DFR,ANS and several transcription factors for anthocyanin synthesis,as well as chlH and CAO in the chlorophyll synthesis pathway by conducting transcriptomic analysis,bulked segregant analysis using both DNA and RNA data,and population genomic analysis.This work provides data for understanding the mechanism of bract pigmentation and will accelerate breeding in developing novel cultivars with richly colored bracts in C.alismatifolia and related species.It is also important to understand the variation in the evolution of the Zingiberaceae family.