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Acetolactate synthase (ALS) inhibitor herbicides are among widely marketed herbicide chemistries that act both against grass and broad-leaved weeds. Sorghum (Sorghum bicolor (L.) Moench) variants carrying resistance to ALS inhibitor herbicides were developed as a post-emergence weed control solution in sorghum. However, some ALS-resistant lines exhibit noticeable interveinal chlorosis at seedling stage, leading to reduced vigor. Although the plants eventually recover at an advanced growth stage, this may be a source of concern for growers and can undermine adoption of the technology. This study was initiated to identify mechanisms related to the manifestation of this phenotype. Two ALS-resistant genotypes, one displaying a yellow phenotype and the other a normal green phenotype, were cultivated, and tissue samples were collected at four time intervals, with the final sampling occurring after the genotypes had fully re-greened. RNA was extracted from the tissue samples and subjected to RNA-Seq analysis. Differential gene expression analysis was carried out using DESeq2, and a selected set of genes were confirmed via qRT-PCR. Gene Ontology enrichment and SorghumCyc pathway analysis uncovered notable regulatory changes in genes associated with chloroplasts, plant defense responses, and hormonal networks in the yellow genotypes. The pattern of gene expression strongly mimicked responses under abiotic stresses. In addition, the findings offer new insights into the potential for sorghum genotypes resistant to environmental stresses to also exhibit tolerance to a range of additional stresses. [ABSTRACT FROM AUTHOR]

Summary: The fungal pathogen, Magnaporthe oryzae Triticum pathotype, causing wheat blast disease was first identified in South America and recently spread across continents to South Asia and Africa. Here, we studied the genetic relationship among isolates found on the three continents.Magnaporthe oryzae strains closely related to a South American field isolate B71 were found to have caused the wheat blast outbreaks in South Asia and Africa. Genomic variation among isolates from the three continents was examined using an improved B71 reference genome and whole‐genome sequences.We found strong evidence to support that the outbreaks in Bangladesh and Zambia were caused by the introductions of genetically separated isolates, although they were all close to B71 and, therefore, collectively referred to as the B71 branch. In addition, B71 branch strains carried at least one supernumerary mini‐chromosome. Genome assembly of a Zambian strain revealed that its mini‐chromosome was similar to the B71 mini‐chromosome but with a high level of structural variation.Our findings show that while core genomes of the multiple introductions are highly similar, the mini‐chromosomes have undergone marked diversification. The maintenance of the mini‐chromosome and rapid genomic changes suggest the mini‐chromosomes may serve important virulence or niche adaptation roles under diverse environmental conditions. [ABSTRACT FROM AUTHOR]

The new variety Betula pendula 'Dalecarlica', selected from Betula pendula , shows high ornamental value owing to its lobed leaf shape. In this study, to identify the genetic components of leaf shape formation, we performed bulked segregant analysis and molecular marker-based fine mapping to identify the causal gene responsible for lobed leaves in B. pendula 'Dalecarlica'. The most significant variations associated with leaf shape were identified within the gene BpPIN1 encoding a member of the PIN-FORMED family, responsible for the auxin efflux carrier. We further confirmed the hypomethylation at the promoter region promoting the expression level of BpPIN1 , which causes stronger and longer veins and lobed leaf shape in B. pendula 'Dalecarlica'. These results indicated that DNA methylation at the BpPIN1 promoter region is associated with leaf shapes in B. pendula. Our findings revealed an epigenetic mechanism of BpPIN1 in the regulation of leaf shape in Betula   Linn. (birch), which could help in the molecular breeding of ornamental traits. [ABSTRACT FROM AUTHOR]

Digestion-ligation-amplification (DLA), a novel adaptor-mediated PCR-based method that uses a single-stranded oligo as the adaptor, was developed to overcome difficulties of amplifying unknown sequences flanking known DNA sequences in large genomes. DLA specifically overcomes the problems associated with existing methods for amplifying genomic sequences flanking Mu transposons, including high levels of nonspecific amplification. Two DLA-based strategies, MuClone and DLA-454, were developed to isolate Mu-tagged alleles. MuClone allows for the amplification of subsets of the numerous Mu transposons in the genome, using unique three-nucleotide tags at the 3? ends of primers, simplifying the identification of flanking sequences that cosegregate with mutant phenotypes caused by Mu insertions. DLA-454, which combines DLA with 454 pyrosequencing, permits the efficient cloning of genes for which multiple independent insertion alleles are available without the need to develop segregating populations. The utility of each approach was validated by independently cloning the gl4 (glossy4) gene. Mutants of gl4 lack the normal accumulation of epicuticular waxes. The gl4 gene is a homolog of the Arabidopsis CUT1 gene, which encodes a condensing enzyme involved in the synthesis of very-long-chain fatty acids, which are precursors of epicuticular waxes.

Although bulked segregant analysis (BSA) has been used extensively in genetic mapping, user-friendly tools which can integrate current algorithms for researchers with no background in bioinformatics are scarce. To address this issue, we developed an R package, PNGSeqR, which takes single-nucleotide polymorphism (SNP) markers from next-generation sequencing (NGS) data in variant call format (VCF) as the input file, provides four BSA algorithms to indicate the magnitude of genome-wide signals, and rapidly defines the candidate region through the permutation test and fractile quantile. Users can choose the analysis methods according to their data and experimental design. In addition, it also supports differential expression gene analysis (DEG) and gene ontology analysis (GO) to prioritize the target gene. Once the analysis is completed, the plots can conveniently be exported. [ABSTRACT FROM AUTHOR]

Postemergence grass weed control continues to be a major challenge in grain sorghum [ Sorghum bicolor (L.) Moench], primarily due to lack of herbicide options registered for use in this crop. The development of herbicide-resistant sorghum technology to facilitate broad-spectrum postemergence weed control can be an economical and viable solution. The 4-hydroxyphenylpyruvate dioxygenase-inhibitor herbicides (e.g., mesotrione or tembotrione) can control a broad spectrum of weeds including grasses, which, however, are not registered for postemergence application in sorghum due to crop injury. In this study, we identified two tembotrione-resistant sorghum genotypes (G-200, G-350) and one susceptible genotype (S-1) by screening 317 sorghum lines from a sorghum association panel (SAP). These tembotrione-resistant and tembotrione-susceptible genotypes were evaluated in a tembotrione dose–response [0, 5.75, 11.5, 23, 46, 92 (label recommended dose), 184, 368, and 736 g ai ha–1] assay. Compared with S-1, the genotypes G-200 and G-350 exhibited 10- and seven fold more resistance to tembotrione, respectively. To understand the inheritance of tembotrione-resistant trait, crosses were performed using S-1 and G-200 or G-350 to generate F1 and F2 progeny. The F1 and F2 progeny were assessed for their response to tembotrione treatment. Genetic analyses of the F1 and F2 progeny demonstrated that the tembotrione resistance in G-200 and G-350 is a partially dominant polygenic trait. Furthermore, cytochrome P450 (CYP)-inhibitor assay using malathion and piperonyl butoxide suggested possible CYP-mediated metabolism of tembotrione in G-200 and G-350. Genotype-by-sequencing based quantitative trait loci (QTL) mapping revealed QTLs associated with tembotrione resistance in G-200 and G-350 genotypes. Overall, the genotypes G-200 and G-350 confer a high level of metabolic resistance to tembotrione and controlled by a polygenic trait. There is an enormous potential to introgress the tembotrione resistance into breeding lines to develop agronomically desirable sorghum hybrids. [ABSTRACT FROM AUTHOR]

Newly emerged wheat blast disease is a serious threat to global wheat production. Wheat blast is caused by a distinct, exceptionally diverse lineage of the fungus causing rice blast disease. Through sequencing a recent field isolate, we report a reference genome that includes seven core chromosomes and mini-chromosome sequences that harbor effector genes normally found on ends of core chromosomes in other strains. No mini-chromosomes were observed in an early field strain, and at least two from another isolate each contain different effector genes and core chromosome end sequences. The mini-chromosome is enriched in transposons occurring most frequently at core chromosome ends. Additionally, transposons in mini-chromosomes lack the characteristic signature for inactivation by repeat-induced point (RIP) mutation genome defenses. Our results, collectively, indicate that dispensable mini-chromosomes and core chromosomes undergo divergent evolutionary trajectories, and mini-chromosomes and core chromosome ends are coupled as a mobile, fast-evolving effector compartment in the wheat pathogen genome. [ABSTRACT FROM AUTHOR]

Cuticular waxes, long-chain hydrocarbon compounds, form the outermost layer of plant surfaces in most terrestrial plants. The presence of cuticular waxes protects plants from water loss and other environmental stresses. Cloning and characterization of genes involved in the regulation, biosynthesis, and extracellular transport of cuticular waxes onto the surface of epidermal cells have revealed the molecular basis of cuticular wax accumulation. However, intracellular trafficking of synthesized waxes to the plasma membrane for cellular secretion is poorly understood. Here, we characterized a maize glossy (gl6) mutant that exhibited decreased epicuticular wax load, increased cuticle permeability, and reduced seedling drought tolerance relative to wild-type. We combined an RNA-sequencing-based mapping approach (BSR-Seq) and chromosome walking to identify the gl6 candidate gene, which was confirmed via the analysis of multiple independent mutant alleles. The gl6 gene represents a novel maize glossy gene containing a conserved, but uncharacterized, DUF538 domain. This study suggests that the GL6 protein may be involved in the intracellular trafficking of cuticular waxes, opening the door to elucidating the poorly understood process by which cuticular wax is transported from its site of biosynthesis to the plasma membrane. [ABSTRACT FROM AUTHOR]

Summary: Epicuticular waxes provide a hydrophobic barrier that protects land plants from environmental stresses. To elucidate the molecular functions of maize glossy mutants that reduce the accumulation of epicuticular waxes, eight non‐allelic glossy mutants were subjected to transcriptomic comparisons with their respective wild‐type siblings. Transcriptomic comparisons identified 2279 differentially expressed (DE) genes. Other glossy genes tended to be down‐regulated in glossy mutants; by contrast stress‐responsive pathways were induced in mutants. Gene co‐expression network (GCN) analysis found that glossy genes were clustered, suggestive of co‐regulation. Genes that potentially regulate the accumulation of glossy gene transcripts were identified via a pathway level co‐expression analysis. Expression data from diverse organs showed that maize glossy genes are generally active in young leaves, silks, and tassels, while largely inactive in seeds and roots. Through reverse genetics, a DE gene homologous to Arabidopsis CER8 and co‐expressed with known glossy genes was confirmed to participate in epicuticular wax accumulation. GCN data‐informed forward genetics approach enabled cloning of the gl14 gene, which encodes a putative membrane‐associated protein. Our results deepen understanding of the transcriptional regulation of the genes involved in the accumulation of epicuticular wax, and provide two maize glossy genes and a number of candidate genes for further characterization. Significance Statement: Co‐expression, suggestive of co‐regulation, of the genes determining accumulation of waxes on the plant's outmost surface was found from gene expression analysis, which also identified transcription factors that are likely to participate in the transcriptional modulation of the wax pathway. With genes co‐expressed with known genes in the pathway, two unknown maize genes responsible for accumulation of surface waxes were experimentally confirmed, demonstrating a strategy to facilitate the identification of causal genes of certain traits. [ABSTRACT FROM AUTHOR]

Aegilops tauschii (2n = 2x = 14, genome DD), also known as Tausch's goatgrass, is the D genome donor of bread or hexaploid wheat Triticum aestivum (2n = 2x = 42, AABBDD genome). It is a rich reservoir of useful genes for biotic and abiotic stress tolerance for wheat improvement. We developed a TILLING (Targeting Induced Local Lesions In Genomes) resource for Ae. tauschii for discovery and validation of useful genes in the D genome of wheat. The population, referred to as TILL-D, was developed with ethyl methanesulfonate (EMS) mutagen. The survival rate in M1 generation was 73%, out of which 22% plants were sterile. In the M2 generation 25% of the planted seeds showed phenotypic mutations such as albinos, chlorinas, no germination, variegated, sterile and partially fertile events, and 2,656 produced fertile M2 plants. The waxy gene was used to calculate the mutation frequency (1/70 kb) of the developed population, which was found to be higher than known mutation frequencies for diploid plants (1/89–1/1000 kb), but lower than that for a polyploid species (1/24–1/51 kb). The TILL-D resource, together with the newly published Ae. tauschii reference genome sequence, will facilitate gene discoveries and validations of agronomically important traits and their eventual fine transfer in bread wheat. [ABSTRACT FROM AUTHOR]

Meiotic recombination is an evolutionary force that generates new genetic diversity upon which selection can act. Whereas multiple studies have assessed genome-wide patterns of recombination and specific cases of intragenic recombination, few studies have assessed intragenic recombination genome-wide in higher eukaryotes. We identified recombination events within or near genes in a population of maize recombinant inbred lines (RILs) using RNA-sequencing data. Our results are consistent with case studies that have shown that intragenic crossovers cluster at the 5′ ends of some genes. Further, we identified cases of intragenic crossovers that generate transgressive transcript accumulation patterns, that is, recombinant alleles displayed higher or lower levels of expression than did nonrecombinant alleles in any of ∼100 RILs, implicating intragenic recombination in the generation of new variants upon which selection can act. Thousands of apparent gene conversion events were identified, allowing us to estimate the genome-wide rate of gene conversion at SNP sites (4.9 × 10−5). The density of syntenic genes (i.e. those conserved at the same genomic locations since the divergence of maize and sorghum) exhibits a substantial correlation with crossover frequency, whereas the density of nonsyntenic genes (i.e. those which have transposed or been lost subsequent to the divergence of maize and sorghum) shows little correlation, suggesting that crossovers occur at higher rates in syntenic genes than in nonsyntenic genes. Increased rates of crossovers in syntenic genes could be either a consequence of the evolutionary conservation of synteny or a biological process that helps to maintain synteny. [ABSTRACT FROM AUTHOR]

Motivation Joint reconstruction of multiple gene regulatory networks (GRNs) using gene expression data from multiple tissues/conditions is very important for understanding common and tissue/condition-specific regulation. However, there are currently no computational models and methods available for directly constructing such multiple GRNs that not only share some common hub genes but also possess tissue/condition-specific regulatory edges. Results In this paper, we proposed a new graphic Gaussian model for joint reconstruction of multiple gene regulatory networks (JRmGRN), which highlighted hub genes, using gene expression data from several tissues/conditions. Under the framework of Gaussian graphical model, JRmGRN method constructs the GRNs through maximizing a penalized log likelihood function. We formulated it as a convex optimization problem, and then solved it with an alternating direction method of multipliers (ADMM) algorithm. The performance of JRmGRN was first evaluated with synthetic data and the results showed that JRmGRN outperformed several other methods for reconstruction of GRNs. We also applied our method to real Arabidopsis thaliana RNA-seq data from two light regime conditions in comparison with other methods, and both common hub genes and some conditions-specific hub genes were identified with higher accuracy and precision. Availability and implementation JRmGRN is available as a R program from: https://github.com/wenpingd. Supplementary information Supplementary data are available at Bioinformatics online. [ABSTRACT FROM AUTHOR]

A correction is presented to the article "Mendelian and Non-Mendelian Regulation of Gene Expression in Maize" which appeared in the February 14, 2018 issue.

The evolution of plant and microbial interactions helps to shape our planet. A major driver of plant and microbial evolution is the selection of beneficial traits borne out of genetic variation. The impact of genetic variation on plant-microbe interactions is well documented, but technological advances have expanded our view of the diversity of genetic variation influencing plant-biotic interactions. The full extent and richness of genomic variation, described here as the dynamic genome, has fueled an amazing array of adaptive traits in plant and microbial populations. In this review, we describe common classes of genetic variation, their mechanisms of generation, examples of their impact on plant-fungal interactions, and technological advancements to define the dynamic genome in plant and fungal systems. • Plant and microbial genomes contain a variety of DNA variation that can impact a single base pair up to several million. • Variation at anyscale of DNA change can alter plant-microbe interactions. • Multiple mechanism are responsible for the creation of different classes of DNA variation. • Advances in DNA characterization and computation are expanding our understanding of genome variation. [ABSTRACT FROM AUTHOR]

The lateral organ boundary domain (LBD) genes encode a group of plant-specific proteins that function as transcription factors in the regulation of plant growth and development. Citrus sinensis lateral organ boundary 1 ( CsLOB1) is a member of the LBD family and functions as a disease susceptibility gene in citrus bacterial canker (CBC). Thirty-four LBD members have been identified from the Citrus sinensis genome. We assessed the potential for additional members of LBD genes in citrus to function as surrogates for CsLOB1 in CBC, and compared host gene expression on induction of different LBD genes. Using custom-designed transcription activator-like (TAL) effectors, two members of the same clade as CsLOB1, named CsLOB2 and CsLOB3, were found to be capable of functioning similarly to CsLOB1 in CBC. RNA sequencing and quantitative reverse transcription-polymerase chain reaction analyses revealed a set of cell wall metabolic genes that are associated with CsLOB1, CsLOB2 and CsLOB3 expression and may represent downstream genes involved in CBC. [ABSTRACT FROM AUTHOR]

Mayetiola destructor is a destructive pest of wheat and has six developmental stages. Molecular mechanisms controlling the transition between developmental stages remain unknown. Here we analyzed genes that were expressed differentially between two successive developmental stages, including larvae at 1, 3, 5, and 7 days, pupae, and adults. A total of 17,344 genes were expressed during one or more of these studied stages. Among the expressed genes, 38–68% were differently expressed between two successive stages, with roughly equal percentages of up- and down-regulated genes. Analysis of the functions of the differentially expressed genes revealed that each developmental stage had some unique types of expressed genes that are characteristic of the physiology at that stage. This is the first genome-wide analysis of genes differentially expressed in different stages in a gall midge. The large dataset of up- and down-regulated genes in each stage of the insect shall be very useful for future research to elucidate mechanisms regulating insect development and other biological processes. [ABSTRACT FROM AUTHOR]

Rathayibacter toxicus is a gram-positive bacterium that infects the floral parts of several Poaceae species in Australia. Bacterial ooze is often produced on the surface of infected plants and bacterial galls are produced in place of seed. R. toxicus is a regulated plant pathogen in the U.S. yet reliable detection and diagnostic tools are lacking. To better understand this geographically-isolated plant pathogen, genetic variation as a function of geographic location, host species, and date of isolation was determined for isolates collected over a forty-year period. Discriminant analyses of recently collected and archived isolates using Multi-Locus Sequence Typing (MLST) and Inter-Simple Sequence Repeats (ISSR) identified three populations of R. toxicus; RT-I and RT-II from South Australia and RT-III from Western Australia. Population RT-I, detected in 2013 and 2014 from the Yorke Peninsula in South Australia, is a newly emerged population of R. toxicus not previously reported. Commonly used housekeeping genes failed to discriminate among the R. toxicus isolates. However, strategically selected and genome-dispersed MLST genes representing an array of cellular functions from chromosome replication, antibiotic resistance and biosynthetic pathways to bacterial acquired immunity were discriminative. Genetic variation among isolates within the RT-I population was less than the within-population variation for the previously reported RT-II and RT-III populations. The lower relative genetic variation within the RT-I population and its absence from sampling over the past 40 years suggest its recent emergence. RT-I was the dominant population on the Yorke Peninsula during the 2013–2014 sampling period perhaps indicating a competitive advantage over the previously detected RT-II population. The potential for introduction of this bacterial plant pathogen into new geographic areas provide a rationale for understanding the ecological and evolutionary trajectories of R. toxicus. [ABSTRACT FROM AUTHOR]