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Our understanding of the past behavior of the geomagnetic field arises from magnetic signals stored in geological materials, e.g., (volcanic) rocks. Bulk rock samples, however, often contain magnetic grains that differ in chemistry, size, and shape; some of them record the Earth's magnetic field well, others are unreliable. The presence of a small amount of adverse behaved magnetic grains in a sample may already obscure important information on the past state of the geomagnetic field. Recently it was shown that it is possible to determine magnetizations of individual grains in a sample by combining X-ray computed tomography and magnetic surface scanning measurements. Here we establish this new Micromagnetic Tomography (MMT) technique and make it suitable for use with different magnetic scanning techniques, and for both synthetic and natural samples. We acquired reliable magnetic directions by selecting subsets of grains in a synthetic sample, and we obtained rock-magnetic information of individual grains in a volcanic sample. This illustrates that MMT opens up entirely new venues of paleomagnetic and rock-magnetic research. MMT's unique ability to determine the magnetization of individual grains in a nondestructive way allows for a systematic analysis of how geological materials record and retain information on the past state of the Earth's magnetic field. Moreover, by interpreting only the contributions of known magnetically well-behaved grains in a sample, MMT has the potential to unlock paleomagnetic information from even the most complex, crucial, or valuable recorders that current methods are unable to recover., Applied Geophysics and Petrophysics

Magnetite and hematite mixtures occur widely in nature. Magnetic unmixing of the signals recorded by these minerals can be important for assessing the origin of their respective paleomagnetic remanences and for extracting geological and paleoenvironmental information. However, unmixing magnetic signals from complex magnetite and hematite mixtures is difficult because of the weak magnetization and high coercivity of hematite. We assess here the relative effectiveness of first-order reversal curve (FORC) and extended FORC-type diagrams, FORC-principal component analysis (PCA), isothermal remanent magnetization (IRM) curve decomposition, and PCA of remanent hysteretic curves for unmixing magnetic components in samples from the magnetically complex Inuyama red chert, Japan. We also further characterize the domain state and coercivity distributions of both magnetite and hematite with FORC-PCA and IRM acquisition analysis in the red chert. We show that IRM curve decomposition can provide valuable component-specific information linked to coercivity, while FORC-PCA enables effective magnetic domain state identification. PCA of remanent hysteretic curves provides useful information about the most significant factors influencing remanence variations and subtle coercivity changes. To identify components in complex magnetite and hematite mixtures, we recommend PCA analysis of remanent hysteretic curves combined with FORC analysis of representative samples to identify domain states and coercivity distributions.

Over the last two centuries, breeders have drastically modified the fruit quality of strawberries through artificial selection. However, there remains significant variation in quality across germplasm with scope for further improvements to be made. We reported extensive phenotyping of fruit quality and yield traits in a multi-parental strawberry population to allow genomic prediction and quantitative trait nucleotide (QTN) identification, thereby enabling the description of genetic architecture to inform the efficacy of implementing advanced breeding strategies. A negative relationship (r = -0.21) between total soluble sugar content and class one yield was identified, indicating a trade-off between these two essential traits. This result highlighted an established dilemma for strawberry breeders and a need to uncouple the relationship, particularly under June-bearing, protected production systems comparable to this study. A large effect of quantitative trait nucleotide was associated with perceived acidity and pH whereas multiple loci were associated with firmness. Therefore, we recommended the implementation of both marker assisted selection (MAS) and genomic prediction to capture the observed variation respectively. Furthermore, we identified a large effect locus associated with a 10% increase in the number of class one fruit and a further 10 QTN which, when combined, are associated with a 27% increase in the number of marketable strawberries. Ultimately, our results suggested that the best method to improve strawberry yield is through selecting parental lines based upon the number of marketable fruits produced per plant. Not only were strawberry number metrics less influenced by environmental fluctuations, but they had a larger additive genetic component when compared with mass traits. As such, selecting using "number" traits should lead to faster genetic gain.

Fusarium oxysporum is a soilborne fungal plant pathogen responsible for causing disease in many economically important crops with “special forms” (formae speciales) adapted to infect specific plant hosts. F. oxysporum f. sp. pisi (FOP) is the causal agent of Fusarium wilt disease of pea. It has been reported in every country where peas are grown commercially. Disease is generally controlled using resistant cultivars possessing single major gene resistance and therefore there is a constant risk of breakdown. The main aim of this work was to characterise F. oxysporum isolates collected from diseased peas in the United Kingdom as well as FOP isolates obtained from other researchers representing different races through sequencing of a housekeeping gene and the presence of Secreted In Xylem (SIX) genes, which have previously been associated with pathogenicity in other F. oxysporum f. spp. F. oxysporum isolates from diseased United Kingdom pea plants possessed none or just one or two known SIX genes with no consistent pattern of presence/absence, leading to the conclusion that they were foot-rot causing isolates rather than FOP. In contrast, FOP isolates had different complements of SIX genes with all those identified as race 1 containing SIX1, SIX6, SIX7, SIX9, SIX10, SIX11, SIX12, and SIX14. FOP isolates that were identified as belonging to race 2 through testing on differential pea cultivars, contained either SIX1, SIX6, SIX9, SIX13, SIX14 or SIX1, SIX6, SIX13. Significant upregulation of SIX genes was also observed in planta over the early stages of infection by different FOP races in pea roots. Race specific SIX gene profiling may therefore provide potential targets for molecular identification of FOP races but further research is needed to determine whether variation in complement of SIX genes in FOP race 2 isolates results in differences in virulence across a broader set of pea differential cultivars.

Bacterial canker of Prunus, affecting economically important stone fruit crops including cherry, peach, apricot and plum, is caused by the plant pathogen Pseudomonas syringae (P.s.). Strains from two pathovars—P.s. pv. syringae (Pss) and P.s. pv. morsprunorum race 1 (PsmR1) and 2 (PsmR2)— in three phylogenetically distant clades have convergently evolved to infect Prunus. The bacteria enter woody tissues through wounds and leaf scars, causing black necrotic cankers. Symptoms are also produced on blossom, fruit and leaves. Little is known about the mechanisms P.s. uses to colonise tree hosts such as Prunus. Here, we created transposon (Tn) mutant libraries in one strain of P.s. from each of the three clades and screened the mutants on immature cherry fruit to look for changes in virulence. Mutants (242) with either reduced or enhanced virulence were detected and further characterised by in vitro screens for biofilm formation, swarming ability, and pathogenicity on leaves and cut shoots. In total, 18 genes affecting virulence were selected, and these were involved in diverse functions including motility, type III secretion, membrane transport, amino acid synthesis, DNA repair and primary metabolism. Interestingly, mutation of the effector gene, hopAU1, led to an increase in virulence of Psm R2.

Microorganisms need to adapt to environmental changes, and genome plasticity can lead to rapid adaptation to hostile environments by increasing genetic diversity. Here, we investigate genome plasticity in the CTG(Ser1) yeast Scheffersomyces stipitis, an organism with an enormous potential for second-generation biofuel production. We demonstrate that S. stipitis has an intrinsically plastic genome and that different S. stipitis isolates have genomes with distinct chromosome organizations. Real-time evolution experiments show that S. stipitis genome plasticity is common and rapid since extensive genomic changes with fitness benefits are detected following in vitro evolution experiments. Hybrid MinION Nanopore and Illumina genome sequencing identify retrotransposons as major drivers of genome diversity. Indeed, the number and position of retrotransposons are different in different S. stipitis isolates, and retrotransposon-rich regions of the genome are sites of chromosome rearrangements. Our findings provide important insights into the adaptation strategies of the CTG(Ser1) yeast clade and have critical implications in the development of second-generation biofuels. These data highlight that genome plasticity is an essential factor for developing sustainable S. stipitis platforms for second-generation biofuels production.

Phytophthora cactorum is often described as a generalist pathogen, with isolates causing disease in a range of plant species. It is the causative agent of two diseases in the cultivated strawberry, crown rot (CR; causing whole plant collapse) and leather rot (LR; affecting the fruit). In the cultivated apple, P. cactorum causes girdling bark rots on the scion (collar rot) and rootstock (crown rot), as well as necrosis of the fine root system (root rot) and fruit rots. We investigated evidence for host specialisation within P. cactorum through comparative genomic analysis of 18 isolates. Whole genome phylogenetic analysis provided genomic support for discrete lineages within P. cactorum, with well-supported non-recombining clades for strawberry CR and apple infecting isolates specialised to strawberry crowns and apple tissue. Isolates of strawberry CR are genetically similar globally, while there is more diversity in apple-infecting isolates. We sought to identify the genetic basis of host specialisation, demonstrating gain and loss of effector complements within the P. cactorum phylogeny, representing putative determinants of host boundaries. Transcriptomic analysis highlighted that those effectors found to be specific to a single host or expanded in the strawberry lineage are amongst those most highly expressed during infection of strawberry and give a wider insight into the key effectors active during strawberry infection. Many effectors that had homologues in other Phytophthoras that have been characterised as avirulence genes were present but not expressed in our tested isolate. Our results highlight several RxLR-containing effectors that warrant further investigation to determine whether they are indeed virulence factors and host-specificity determinants for strawberry and apple. Furthermore, additional work is required to determine whether these effectors are suitable targets to focus attention on for future resistance breeding efforts.

Copyright © 2020 The Authors, some rights reserved; exclusive licensee American Association for the Advancement of Science. No claim to original U.S. Government Works. Distributed under a Creative Commons Attribution NonCommercial License 4.0 (CC BY-NC). The time of origin of the geodynamo has important implications for the thermal evolution of the planetary interior and the habitability of early Earth. It has been proposed that detrital zircon grains from Jack Hills, Western Australia, provide evidence for an active geodynamo as early as 4.2 billion years (Ga) ago. However, our combined paleomagnetic, geochemical, and mineralogical studies on Jack Hills zircons indicate that most have poor magnetic recording properties and secondary magnetization carriers that postdate the formation of the zircons. Therefore, the existence of the geodynamo before 3.5 Ga ago remains unknown.