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Anthracnose, caused by the fungal pathogen Colletotrichum spp., is one of the most significant tomato diseases in the United States and worldwide. No commercial cultivars with anthracnose resistance are available, limiting resistant breeding. Cultivars with genetic resistance would significantly reduce crop losses, reduce the use of fungicides, and lessen the risks associated with chemical application. A recombinant inbred line (RIL) mapping population (N=243) has been made from a cross between the susceptible US28 cultivar and the resistant but semiwild and small-fruited 95L368 to identify quantitative trait loci (QTLs) associated with anthracnose resistance. The RIL population was phenotyped for resistance by inoculating ripe field-harvested tomato fruits with Colletotrichum coccodes for two seasons. In this study, we identified twenty QTLs underlying resistance, with a range of phenotypic variance of 4.5 to 17.2% using a skeletal linkage map and a GWAS. In addition, a QTLseq analysis was performed using deep sequencing of extreme bulks that validated QTL positions identified using traditional mapping and resolved candidate genes underlying various QTLs. We further validated AP2-like ethylene-responsive transcription factor, N-alpha-acetyltransferase (NatA), cytochrome P450, amidase family protein, tetratricopeptide repeat, bHLH transcription factor, and disease resistance protein RGA2-like using PCR allelic competitive extension (PACE) genotyping. PACE assays developed in this study will enable high-throughput screening for use in anthracnose resistance breeding in tomato. [ABSTRACT FROM AUTHOR]

Tree crops are explored for food sources and raw materials for industrial sectors. However, breeding tree species to meet current economic demands amid forecasts of agricultural resource scarcity and climate instability is a challenging task. This is especially true due to their long juvenile phase, often difficulties related to reproductive biology, and scarcity of genetic resources, which largely delays phenotyping and selection of segregating populations. On the other hand, genome sequence and transcriptomic data are becoming increasingly available for perennial crops, along with optimized protocols for genetic transformation and in vitro regeneration. Due to the development of these fields altogether and the advances in gene editing technologies, it is now possible to glimpse the design of tree crops with optimized traits for cultivation. We review the status of genome projects and the application of CRISPR-Cas-based systems in tree crops, alongside an exploration of gene editing technologies to develop perennial crop ideotypes. Herein, we seek to raise attention to the capabilities and potential of crop designing applied to tree species and to the opportunity that we have, as a society, to create stepwise strategies to tailor the breeding of perennial crops in the context of the current environmental challenges and increasing population demands. [ABSTRACT FROM AUTHOR]

MADS-box transcription factors (TFs) are involved in multiple plant development processes and are most known during the reproductive transition and floral organ development. Very few genes have been characterized in the genome of Humulus lupulus L. (Cannabaceae), an important crop for the pharmaceutical and beverage industries. The MADS-box family has not been studied in this species yet. We identified 65 MADS-box genes in the hop genome, of which 29 encode type-II TFs (27 of subgroup MIKCC and 2 MIKC*) and 36 type-I proteins (26 α, 9 β, and 1 γ). Type-II MADS-box genes evolved more complex architectures than type-I genes. Interestingly, we did not find FLOWERING LOCUS C (FLC) homologs, a transcription factor that acts as a floral repressor and is negatively regulated by cold. This result provides a molecular explanation for a previous work showing that vernalization is not a requirement for hop flowering, which has implications for its cultivation in the tropics. Analysis of gene ontology and expression profiling revealed genes potentially involved in the development of male and female floral structures based on the differential expression of ABC homeotic genes in each whorl of the flower. We identified a gene exclusively expressed in lupulin glands, suggesting a role in specialized metabolism in these structures. In toto, this work contributes to understanding the evolutionary history of MADS-box genes in hop, and provides perspectives on functional genetic studies, biotechnology, and crop breeding. [ABSTRACT FROM AUTHOR]

Background: Species in the Solanaceae family are known for producing plethora of specialized metabolites. In addition to biosynthesis pathways, a full comprehension of secondary metabolism must also take into account the transport and subcellular compartmentalization of substances. Here, we examined the MATE (Multidrug and Toxic Compound Extrusion, or Multi-Antimicrobial Extrusion) gene family in the tomato (Solanum lycopersicum) genome with the objective of better understanding the transport of secondary metabolites in this model species. MATE membrane effluxers encompass an ancient gene family of secondary transporters present in all kingdoms of life, but with a remarkable expansion in plants. They mediate the transport of primary and secondary metabolites using the proton motive force through several membrane systems of the cell. Results: We identified 67 genes coding for MATE transporters in the tomato genome, 33 of which are expressed constitutively whereas 34 are expressed in specific cell types or environmental conditions. Synteny analyses revealed bona fide paralogs and Arabidopsis orthologs. Co-expression analysis between MATE and regulatory genes revealed 78 positive and 8 negative strong associations (ρ≥∣0.8∣). We found no evidence of MATE transporters belonging to known metabolic gene clusters in tomato. Conclusions: Altogether, our expression data, phylogenetic analyses, and synteny study provide strong evidence of functional homologies between MATE genes of tomato and Arabidopsis thaliana. Our co-expression study revealed potential transcriptional regulators of MATE genes that warrant further investigation. This work sets the stage for genome-wide functional analyses of MATE transporters in tomato and other Solanaceae species of economic relevance. [ABSTRACT FROM AUTHOR]