Maize Inbred Line B96 Is the Source of Large-Effect Loci for Resistance to Generalist but Not Specialist Spider Mites

Maize (Zea mays subsp. mays) yield loss from arthropod herbivory is substantial. While the basis of resistance to major insect herbivores has been comparatively well-studied in maize, less is known about resistance to spider mite herbivores, which are distantly related to insects and feed by a different mechanism. Two spider mites, the generalist Tetranychus urticae, and the grass-specialist Oligonychus pratensis, are notable pests of maize, especially during drought conditions. We assessed resistance (antibiosis) to both mites of 38 highly diverse maize lines, including several previously reported to be resistant to one or the other mite species. We found that line B96, as well as its derivatives B49 and B75, were highly resistant to T. urticae. In contrast, neither these three lines, nor any others included in our study, were notably resistant to the specialist O. pratensis. Quantitative trait locus (QTL) mapping with replicate populations from crosses of B49, B75, and B96 to susceptible B73 identified a QTL in the same genomic interval on chromosome 6 for T. urticae resistance in each of the three resistant lines, and an additional resistance QTL on chromosome 1 was unique to B96. Single-locus genotyping with a marker coincident with the chromosome 6 QTL in crosses of both B49 and B75 to B73 revealed that the respective QTL was large-effect; it explained ∼70% of the variance in resistance, and resistance alleles from B49 and B75 acted recessively as compared to B73. Finally, a genome-wide haplotype analysis using genome sequence data generated for B49, B75, and B96 identified an identical haplotype, likely of initial origin from B96, as the source of T. urticae resistance on chromosome 6 in each of the B49, B75, and B96 lines. Our findings uncover the relationship between intraspecific variation in maize defenses and resistance to its major generalist and specialist spider mite herbivores, and we identified loci for use in breeding programs and for genetic studies of resistance to T. urticae, the most widespread spider mite pest of maize

Ixodes pacificus ticks maintain embryogenesis and egg hatching after antibiotic treatment of Rickettsia endosymbiont.

Rickettsia is a genus of intracellular bacteria that causes a variety of diseases in humans and other mammals and associates with a diverse group of arthropods. Although Rickettsia appears to be common in ticks, most Rickettsia-tick relationships remain generally uncharacterized. The most intimate of these associations is Rickettsia species phylotype G021, a maternally and transstadially transmitted endosymbiont that resides in 100% of I. pacificus in California. We investigated the effects of this Rickettsia phylotype on I. pacificus reproductive fitness using selective antibiotic treatment. Ciprofloxacin was 10-fold more effective than tetracycline in eliminating Rickettsia from I. pacificus, and quantitative PCR results showed that eggs from the ciprofloxacin-treated ticks contained an average of 0.02 Rickettsia per egg cell as opposed to the average of 0.2 in the tetracycline-treated ticks. Ampicillin did not significantly affect the number of Rickettsia per tick cell in adults or eggs compared to the water-injected control ticks. We found no relationship between tick embryogenesis and rickettsial density in engorged I. pacificus females. Tetracycline treatment significantly delayed oviposition of I. pacificus ticks, but the antibiotic's effect was unlikely related to Rickettsia. We also demonstrated that Rickettsia-free eggs could successfully develop into larvae without any significant decrease in hatching compared to eggs containing Rickettsia. No significant differences in the incubation period, egg hatching rate, and the number of larvae were found between any of the antibiotic-treated groups and the water-injected tick control. We concluded that Rickettsia species phylotype G021 does not have an apparent effect on embryogenesis, oviposition, and egg hatching of I. pacificus

A molecular-genetic understanding of diapause in spider mites : current knowledge and future directions

During unfavourable conditions, many arthropods have the ability to enter into diapause and synchronize their development and reproduction to seasonal patterns. Diapause or winter hibernation in insects and mites is set off by a number of cues, with photoperiod being the most well-defined and strongest signal. This review focuses on the current knowledge of '-omics' data and the genetics of diapause in the two-spotted spider mite Tetranychus urticae, a member of the family Tetranychidae (Arthropoda: Chelicerata: Arachnida: Acari). This species is a serious polyphagous pest and females undergo a reproductive facultative diapause when immature stages are exposed to long nights. Winter hibernation induces different physiological processes characterized by a metabolic suppression, different energy use, increased stress tolerance and the production of cryoprotectants, all initiated by a complex signal transduction pathway. Keto-carotenoids are known to cause the deeply orange colour typical for diapausing females. Furthermore, research with colour mutants of T. urticae has shown the need for carotenoids with respect to the induction of diapause, even though the molecular-genetic mechanisms underlying these colour phenotypes are still unknown. In addition, marked latitudinal variation in diapause incidence among populations has been observed in nature, with modes of inheritance ranging from recessive to dominant, as well as monogenic to polygenic. We end by highlighting the emerging opportunities for functional studies that aim to unravel the complex factors underlying diapause in spider mites

A marker gene-based method for identifying the cell-type of origin from single-cell RNA sequencing data

Single-cell RNA sequencing (scRNA-seq) experiments provide opportunities to peer into complex tissues at single-cell resolution. However, insightful biological interpretation of scRNA-seq data relies upon precise identification of cell types. The ability to identify the origin of a cell quickly and accurately will greatly improve downstream analyses. We present Sargent, a transformation-free, cluster-free, single-cell annotation algorithm for rapidly identifying the cell types of origin based on cell type-specific markers. We demonstrate Sargent's high accuracy by annotating simulated datasets. Further, we compare Sargent performance against expert-annotated scRNA-seq data from human organs including PBMC, heart, kidney, and lung. We demonstrate that Sargent retains both the flexibility and biological interpretability of cluster-based manual annotation. Additionally, the automation eliminates the labor intensive and potentially biased user annotation, producing robust, reproducible, and scalable outputs. • Sargent is a transformation-free, cluster-free, single-cell annotation algorithm for rapidly identifying the cell types of origin based on cell type-specific markers. • Sargent retains both the flexibility and biological interpretability of cluster-based manual annotation. • Automation eliminates the labor intensive and potentially biased user annotation, producing robust, reproducible, and scalable outputs

Kaplan-Meier (time-to-event) plots of the preoviposition period and the incubation periods, and boxplots representing egg hatching rate, and the number of larvae from engorged <i>Ixodes pacificus</i> females.

<p>2A) A Kaplan-Meier plot where each colored line corresponds to the fraction of adult female ticks that had not started laying eggs on a particular day after the ticks were injected with antibiotics or water (control). Vertical dashes on the colored lines represent censorship, where a tick that had not started to lay eggs died and was dropped from the study. The tetracycline group (red) took significantly longer to start laying eggs compared to the rest (<i>P</i><0.05) 2B) A Kaplan-Meier plot where the colored lines represent the proportion of egg samples laid by individual ticks whose eggs had not finished hatching into larvae a certain number of days after oviposition began. 2C) A boxplot showing the hatching rate, or the fraction of tick eggs that successfully hatched into larvae, in the four treatment groups. Each individually colored box represents the hatching rate distribution of eggs laid by each female tick in the group. 2D) A boxplot specifying the distribution of the total number of larvae each female yielded. No significant difference in (C) hatching rate or (D) the number of larvae was present between treatment groups (<i>P</i><0.05). Circles outside the boxes in (C) and (D) represent outliers. The colors in all the plots in the figure correspond to specific treatment groups: blue - ampicillin, yellow - ciprofloxacin, red - tetracycline, green - injection with water (control).</p

Prevalence of infection with <i>Rickettsia</i> species phylotype G021 in <i>Ixodes pacificus</i> egg cohorts of 10 from each of the 14 ticks in the ciprofloxacin-injected group.

<p>Prevalence of infection with <i>Rickettsia</i> species phylotype G021 in <i>Ixodes pacificus</i> egg cohorts of 10 from each of the 14 ticks in the ciprofloxacin-injected group.</p

Data from: Convergent evolution of cytochrome P450s underlies independent origins of keto-carotenoid pigmentation in animals

Keto-carotenoids contribute to many important traits in animals, including vision and coloration. In a great number of animal species, keto-carotenoids are endogenously produced from carotenoids by carotenoid ketolases. Despite the ubiquity and functional importance of keto-carotenoids in animals, the underlying genetic architectures of their production have remained enigmatic. The body and eye colorations of spider mites (Arthropoda: Chelicerata) are determined by β-carotene and keto-carotenoid derivatives. Here, we focus on a carotenoid pigment mutant of the spider mite Tetranychus kanzawai that, as shown by chromatography, lost the ability to produce keto-carotenoids. We employed bulked segregant analysis and linked the causal locus to a single narrow genomic interval. The causal mutation was fine-mapped to a minimal candidate region that held only one complete gene, the cytochrome P450 monooxygenase CYP384A1, of the CYP3 clan. Using a number of genomic approaches, we revealed that an inactivating deletion in the fourth exon of CYP384A1 caused the aberrant pigmentation. Phylogenetic analysis indicated that CYP384A1 is orthologous across mite species of the ancient Trombidiformes order where carotenoids typify eye and body coloration, suggesting a deeply conserved function of CYP384A1 as a carotenoid ketolase. Previously, CYP2J19, a cytochrome P450 of the CYP2 clan, has been identified as a carotenoid ketolase in birds and turtles. Our study shows that selection for endogenous production of keto-carotenoids led to convergent evolution whereby cytochrome P450s were independently co-opted in vertebrate and invertebrate animal lineages

Trans-driven variation in expression is common among detoxification genes in the extreme generalist herbivore Tetranychus urticae.

The extreme adaptation potential of the generalist herbivore Tetranychus urticae (the two-spotted spider mite) to pesticides as well as diverse host plants has been associated with clade-specific gene expansions in known detoxifying enzyme families, and with extensive and rapid transcriptional responses. However, how this broad transcriptional potential is regulated remains largely unknown. Using a parental/F1 design in which four inbred strains were crossed to a common inbred strain, we assessed the genetic basis and inheritance of gene expression variation in T. urticae. Mirroring known phenotypic variation in the progenitor strains of the inbreds, we confirmed that the inbred strains we created were genetically distinct, varied markedly in pesticide resistance, and also captured variation in host plant fitness as is commonly observed in this species. By examining differences in gene expression between parents and allele-specific expression in F1s, we found that variation in RNA abundance was more often explained in trans as compared to cis, with the former associated with dominance in inheritance. Strikingly, in a gene ontology analysis, detoxification genes of the cytochrome P450 monooxygenase (CYP) family, as well as dioxygenases (DOGs) acquired from horizontal gene transfer from fungi, were specifically enriched at the extremes of trans-driven up- and downregulation. In particular, multiple CYPs and DOGs with broad substrate-specificities for pesticides or plant specialized compounds were exceptionally highly upregulated as a result of trans-regulatory variation, or in some cases synergism of cis and trans, in the most multi-pesticide resistant strains. Collectively, our findings highlight the potential importance of trans-driven expression variation in genes associated with xenobiotic metabolism and host plant use for rapid adaptation in T. urticae, and also suggests modular control of these genes, a regulatory architecture that might ameliorate negative pleiotropic effects

Disruption of a horizontally transferred phytoene desaturase abolishes carotenoid accumulation and diapause in Tetranychus urticae

Carotenoids underlie many of the vibrant yellow, orange, and red colors in animals, and are involved in processes ranging from vision to protection from stresses. Most animals acquire carotenoids from their diets because de novo synthesis of carotenoids is primarily limited to plants and some bacteria and fungi. Recently, sequencing projects in aphids and adelgids, spider mites, and gall midges identified genes with homology to fungal sequences encoding de novo carotenoid biosynthetic proteins like phytoene desaturase. The finding of horizontal gene transfers of carotenoid biosynthetic genes to three arthropod lineages was unprecedented; however, the relevance of the transfers for the arthropods that acquired them has remained largely speculative, which is especially true for spider mites that feed on plant cell contents, a known source of carotenoids. Pigmentation in spider mites results solely from carotenoids. Using a combination of genetic approaches, we show that mutations in a single horizontally transferred phytoene desaturase result in complete albinism in the twospotted spider mite, Tetranychus urticae, as well as in the citrus red mite, Panonychus citri. Further, we show that phytoene desaturase activity is essential for photoperiodic induction of diapause in an overwintering strain of T. urticae, consistent with a role for this enzyme in provisioning provitamin A carotenoids required for light perception. Carotenoid biosynthetic genes of fungal origin have therefore enabled some mites to forgo dietary carotenoids, with endogenous synthesis underlying their intense pigmentation and ability to enter diapause, a key to the global distribution of major spider mite pests of agriculture