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Meiotic crossovers (COs) ensure proper chromosome segregation and redistribute the genetic variation that is transmitted to the next generation. Large populations and the demand for genome-wide, fine-scale resolution challenge existing methods for CO identification. Taking advantage of linked-read sequencing, we develop a highly efficient method for genome-wide identification of COs at kilobase resolution in pooled recombinants. We first test this method using a pool of Arabidopsis F2 recombinants, and recapitulate results obtained from the same plants using individual whole-genome sequencing. By applying this method to a pool of pollen DNA from an F1 plant, we establish a highly accurate CO landscape without generating or sequencing a single recombinant plant. The simplicity of this approach enables the simultaneous generation and analysis of multiple CO landscapes, accelerating the pace at which mechanisms for the regulation of recombination can be elucidated through efficient comparisons of genotypic and environmental effects on recombination.

In plants, CG DNA methylation is prevalent in the transcribed regions of many constitutively expressed genes (gene body methylation; gbM), but the origin and function of gbM remain unknown. Here we report the discovery that Eutrema salsugineum has lost gbM from its genome, to our knowledge the first instance for an angiosperm. Of all known DNA methyltransferases, only CHROMOMETHYLASE 3 (CMT3) is missing from E. salsugineum Identification of an additional angiosperm, Conringia planisiliqua, which independently lost CMT3 and gbM, supports that CMT3 is required for the establishment of gbM. Detailed analyses of gene expression, the histone variant H2A.Z, and various histone modifications in E. salsugineum and in Arabidopsis thaliana epigenetic recombinant inbred lines found no evidence in support of any role for gbM in regulating transcription or affecting the composition and modification of chromatin over evolutionary timescales.

Solanum pennellii is a wild tomato species endemic to Andean regions in South America, where it has evolved to thrive in arid habitats. Because of its extreme stress tolerance and unusual morphology, it is an important donor of germplasm for the cultivated tomato Solanum lycopersicum. Introgression lines (ILs) in which large genomic regions of S. lycopersicum are replaced with the corresponding segments from S. pennellii can show remarkably superior agronomic performance. Here we describe a high-quality genome assembly of the parents of the IL population. By anchoring the S. pennellii genome to the genetic map, we define candidate genes for stress tolerance and provide evidence that transposable elements had a role in the evolution of these traits. Our work paves a path toward further tomato improvement and for deciphering the mechanisms underlying the myriad other agronomic traits that can be improved with S. pennellii germplasm.

Retrotransposons are mobile genetic elements that populate chromosomes, where the host largely controls their activities (1-3). In plants and mammals, retrotransposons are transcriptionally silenced by DNA methylation (1,4), which in Arabidopsis is propagated at CG dinucleotides by METHYLTRANSFERASE 1 (METl)s. In metl mutants, however, mobilization of retrotransposons is not observed, despite their transcriptional activation (4-6). A posttranscriptional mechanism therefore seems to be preventing retrotransposition. Here we show that a copia-type retrotransposon (Evade, French for 'fugitive') evaded suppression of its movement during inbreeding of hybrid epigenomes consisting of metl- and wild-type-derived chromosomes. Evade (EVD) reinsertions caused a series of developmental mutations that allowed its identification. Genetic testing of host control of the EVD life cycle showed that transcriptional suppression occurred by CG methylation supported by RNA-directed DNA methylation. On transcriptional reactivation, subsequent steps of the EVD rycle were inhibited by plant-specific RNA polymerase IV/V (7,8) and the histone methyltransferase KRYPTONITE (KYP). Moreover, genome resequencing demonstrated retrotransposition of EVD but no other potentially active retroelements when this combination of epigenetic mechanisms was compromised. Our results demonstrate that epigenetic control of retrotransposons extends beyond transcriptional suppression and can be individualized for particular elements., We established a population of epigenetic recombinant inbred lines (epiRILs) derived from a cross between a wild-type (WT) and a metl homozygous plant carrying a null mutation for METI (metl [...]

Summary: Arabis alpina is a polycarpic perennial, in which PERPETUAL FLOWERING1 (PEP1) regulates flowering and perennial traits in a vernalization‐dependent manner. Mutagenesis screens of the pep1 mutant established the role of other flowering time regulators in PEP1‐parallel pathways.Here we characterized three allelic enhancers of pep1 (eop002, 085 and 091) which flower early. We mapped the causal mutations and complemented mutants with the identified gene. Using quantitative reverse transcriptase PCR and reporter lines, we determined the protein spatiotemporal expression patterns and localization within the cell. We also characterized its role in Arabidopsis thaliana using CRISPR and in A. alpina by introgressing mutant alleles into a wild‐type background.These mutants carried lesions in an AAA+ ATPase of unknown function, FLOWERING REPRESSOR AAA+ATPase 1 (AaFRAT1). AaFRAT1 was detected in the vasculature of young leaf primordia and the rib zone of flowering shoot apical meristems. At the subcellular level, AaFRAT1 was localized at the interphase between the endoplasmic reticulum and peroxisomes. Introgression lines carrying Aafrat1 alleles required less vernalization to flower and reduced number of vegetative axillary branches. By contrast, A. thaliana CRISPR lines showed weak flowering phenotypes.AaFRAT1 contributes to flowering time regulation and the perennial growth habit of A. alpina. [ABSTRACT FROM AUTHOR]

SUMMARY: Loss‐of‐function alleles of plant MLO genes confer broad‐spectrum resistance to powdery mildews in many eudicot and monocot species. Although barley (Hordeum vulgare) mlo mutants have been used in agriculture for more than 40 years, understanding of the molecular principles underlying this type of disease resistance remains fragmentary. Forward genetic screens in barley have revealed mutations in two Required for mlo resistance (Ror) genes that partially impair immunity conferred by mlo mutants. While Ror2 encodes a soluble N‐ethylmaleimide‐sensitive factor‐attached protein receptor (SNARE), the identity of Ror1, located at the pericentromeric region of barley chromosome 1H, remained elusive. We report the identification of Ror1 based on combined barley genomic sequence information and transcriptomic data from ror1 mutant plants. Ror1 encodes the barley class XI myosin Myo11A (HORVU.MOREX.r3.1HG0046420). Single amino acid substitutions of this myosin, deduced from non‐functional ror1 mutant alleles, map to the nucleotide‐binding region and the interface between the relay‐helix and the converter domain of the motor protein. Ror1 myosin accumulates transiently in the course of powdery mildew infection. Functional fluorophore‐labeled Ror1 variants associate with mobile intracellular compartments that partially colocalize with peroxisomes. Single‐cell expression of the Ror1 tail region causes a dominant‐negative effect that phenocopies ror1 loss‐of‐function mutants. We define a myosin motor for the establishment of mlo‐mediated resistance, suggesting that motor protein‐driven intracellular transport processes are critical for extracellular immunity, possibly through the targeted transfer of antifungal and/or cell wall cargoes to pathogen contact sites. Significance Statement: We report the identification of a barley (Hordeum vulgare) gene that is required for the agriculturally relevant broad‐spectrum powdery mildew resistance conditioned by mlo mutants. The gene encodes a class XI myosin motor protein that partly associates with peroxisomes and might be needed for the timely intracellular transport of defense‐related cargoes in the context of extracellular immunity. [ABSTRACT FROM AUTHOR]