Disentangling the genetic basis of rhizosphere microbiome assembly in tomato

Microbiomes play a pivotal role in plant growth and health, but the genetic factors involved in microbiome assembly remain largely elusive. Here, 16S amplicon and metagenomic features of the rhizosphere microbiome were mapped as quantitative traits of a recombinant inbred line population of a cross between wild and domesticated tomato. Gene content analysis of prioritized tomato QTLs suggested a genetic basis for differential recruitment of various rhizobacterial lineages, including a Streptomyces-associated 6.31-Mbp region harboring tomato domestication sweeps and encoding, among others, the iron regulator FIT and the aquaporin SlTIP2.3. Within metagenome-assembled genomes of the rhizobacterial lineages Streptomyces and Cellvibrio, we identified microbial genes involved in metabolism of plant polysaccharides, iron, sulfur, trehalose, and vitamins, whose genetic variation associated with either modern or wild tomato QTLs. Integrating 'microbiomics' and quantitative plant genetics pinpointed putative plant and reciprocal microbial traits underlying microbiome assembly, thereby providing the first step towards plant-microbiome breeding programs.

Tomato Landraces Are Competitive with Commercial Varieties in Terms of Tolerance to Plant Pathogens—A Case Study of Hungarian Gene Bank Accessions on Organic Farms

Landraces are generally neglected by industrialized agriculture, regardless of their potential to provide valuable genetic material for breeding and to diversifying the available assortment for producers and markets. They may also excel in certain plant protection issues with possible resistance or tolerance to plant pathogens. This is the first report on the disease susceptibility traits of Hungarian on certain indeterminate and determinate tomato gene bank accessions under on-farm organic conditions. For this, a three-year on-farm experiment was conducted in two management systems, open-field and protected. Yield and disease symptoms data obtained from ten tomato landraces were compared to commercial varieties. The incidence and severity of three important diseases (caused by late blight ‘Phytophthora infestans’, early blight ‘Alternaria solani’ and Septoria leafspot ‘Septoria lycopersici’), as well as yield, were recorded and assessed. According to these results, there were no significant difference between landraces and control varieties (San Marzano, Kecskeméti 549) regarding the studied parameters, and year was a determinant factor in the occurrence and severity of the infection of the studied diseases. In 2016, rainy, humid weather induced a severe late blight infection, causing serious damage to the open field, while the weather in 2015 and 2017 was favorable for tomato production and our measurements. There were some differences within and between landraces in terms of susceptibility. The investigation revealed that certain accessions can be highly recommended, e.g., the indeterminate ‘Fadd’ (RCAT030275) and ‘Mátrafüred’ (RCAT057656) had suitably high yields with significantly lower susceptibility to late blight, and the determinate ‘Szentlőrinckáta’ (RCAT078726) with high yield as well as tolerance to early blight is also recommendable, but it is sensitive to late blight under an adverse environment. This study suggests that landraces are competitive with the studied commercial varieties under organic production systems. Considering yield and the prevention of the major diseases of tomato, the studied tomato gene bank accessions are recommended for organic field and protected management systems.

Evolution of a plant gene cluster in Solanaceae and emergence of metabolic diversity

Plants produce phylogenetically and spatially restricted, as well as structurally diverse specialized metabolites via multistep metabolic pathways. Hallmarks of specialized metabolic evolution include enzymatic promiscuity and recruitment of primary metabolic enzymes and examples of genomic clustering of pathway genes. Solanaceae glandular trichomes produce defensive acylsugars, with sidechains that vary in length across the family. We describe a tomato gene cluster on chromosome 7 involved in medium chain acylsugar accumulation due to trichome specific acyl-CoA synthetase and enoyl-CoA hydratase genes. This cluster co-localizes with a tomato steroidal alkaloid gene cluster and is syntenic to a chromosome 12 region containing another acylsugar pathway gene. We reconstructed the evolutionary events leading to this gene cluster and found that its phylogenetic distribution correlates with medium chain acylsugar accumulation across the Solanaceae. This work reveals insights into the dynamics behind gene cluster evolution and cell-type specific metabolite diversity.

Evolution of a plant gene cluster in Solanaceae and emergence of metabolic diversity

Plants produce phylogenetically and spatially restricted, as well as structurally diverse specialized metabolites via multistep metabolic pathways. Hallmarks of specialized metabolic evolution include enzymatic promiscuity, recruitment of primary metabolic enzymes and genomic clustering of pathway genes. Solanaceae plant glandular trichomes produce defensive acylsugars, with aliphatic sidechains that vary in length across the family. We describe a tomato gene cluster on chromosome 7 involved in medium chain acylsugar accumulation due to trichome specific acyl-CoA synthetase and enoyl-CoA hydratase genes. This cluster co-localizes with a tomato steroidal alkaloid gene cluster forming a ‘supercluster’, and is syntenic to a chromosome 12 region containing another acylsugar pathway gene. We reconstructed the evolutionary events leading to emergence of this gene cluster and found that its phylogenetic distribution correlates with medium chain acylsugar accumulation across the Solanaceae. This work reveals dynamics behind emergence of novel enzymes from primary metabolism, gene cluster evolution and cell-type specific metabolite diversity.

Expression and distribution of PIEZO1 in the mouse urinary tract

The proper function of the organs that make up the urinary tract (kidneys, ureters, bladder, and urethra) depends on their ability to sense and respond to mechanical forces, including shear stress and wall tension. However, we have limited understanding of the mechanosensors that function in these organs and the tissue sites in which these molecules are expressed. Possible candidates include stretch-activated PIEZO channels (PIEZO1 and PIEZO2), which have been implicated in mechanically regulated body functions including touch sensation, proprioception, lung inflation, and blood pressure regulation. Using reporter mice expressing a COOH-terminal fusion of Piezo1 with the sequence for the tandem-dimer Tomato gene, we found that PIEZO1 is expressed in the kidneys, ureters, bladder, and urethra as well as organs in close proximity, including the prostate, seminal vesicles and ducts, ejaculatory ducts, and the vagina. We further found that PIEZO1 expression is not limited to one cell type; it is observed in the endothelial and parietal cells of the renal corpuscle, the basolateral surfaces of many of the epithelial cells that line the urinary tract, the interstitial cells of the bladder and ureters, and populations of smooth and striated muscle cells. We propose that in the urinary tract, PIEZO1 likely functions as a mechanosensor that triggers responses to wall tension.

SLTAB2 is the paramutated SULFUREA locus in tomato

The sulfurea (sulf) allele is a silent epigenetic variant of a tomato gene (Solanum lycopersicum) affecting pigment production. It is homozygous lethal but, in a heterozygote sulf /+, the wild type allele undergoes silencing so that the plants exhibit chlorotic sectors. This transfer of the silenced state between alleles resembles the process of paramutation that is best characterised in maize. To understand the mechanism of paramutation we mapped SULF to the ortholog SLTAB2 of an Arabidopsis gene that, consistent with the pigment deficiency, is involved in the translation of photosystem I. Paramutation of SLTAB2 is linked to an increase in DNA methylation and production of small interfering RNAs at its promoter. Virus-induced gene silencing of SLTAB2 phenocopies sulf consistent with the possibility that siRNAs mediate the paramutation of SULFUREA. Unlike the maize systems the paramutagenicity of sulf is not, however, associated with repeated sequences at the region of siRNA production or DNA methylation.