Horticultural crops include a diverse array of crops comprising fruits, vegetables, nuts, flowers, aromatic and medicinal plants. They provide nutritional, medicinal, and aesthetic benefits to mankind. However, these crops undergo many biotic (e.g., diseases, pests) and abiotic stresses (e.g., drought, salinity). Conventional breeding strategies to improve traits in crops involve the use of a series of backcrossing and selection for introgression of a beneficial trait into elite germplasm, which is time and resource consuming. Recent new plant breeding tools such as clustered regularly interspaced short palindromic repeats (CRISPR) /CRISPR-associated protein-9 (Cas9) technique have the potential to be rapid, cost-effective, and precise tools for crop improvement. In this review article, we explore the CRISPR/Cas9 technology, its history, classification, general applications, specific uses in horticultural crops, challenges, existing resources, associated regulatory aspects, and the way forward.

Bacterial diseases pose a severe challenge to growers and cause significant loss to the billion-dollar onion industry in the United States. Texas is the sixth largest onion producing state, yet the bacterial communities associated with short-day onion crops grown in Texas have not been studied. This study was conducted to identify, characterize, and understand the diversity of bacteria associated with onion production in Texas. In 2020, 190 foliar and 210 bulb samples were collected from onion crops in the Rio Grande Valley and Winter Garden regions of Texas. Sequencing of the 16s rRNA gene was used to identify each bacterial strains to a genus. The pathogenicity to onion of each bacterial strain was tested using three assays: a red onion scale assay, a yellow onion bulb assay, and a foliar assay. Whole genome sequencing was done to identify the onion-pathogenic strains to species. Collectively, isolates of 24 genera belonging to three phyla were detected, including 19 genera from foliar samples and nine genera from bulb samples. Isolates in the Phylum Proteobacteria, including 15 genera of Gram-negative bacteria, were the most abundant of the taxa, comprising 90.0% of the strains isolated. The diversity of foliar isolates was evenly distributed between Gram-positive and Gram-negative bacteria, while Gram-negative bacteria dominated the isolates from bulb samples. In total, 83.9% of the bacterial isolates were not pathogenic on onion, with only isolates of Pantoea, Pseudomonas, Burkholderia, Erwinia, Enterobacter, and Curtobacterium proving pathogenic. Strains of Burkholderia gladioli, Pseudomonas alliivorans, Pantoea agglomerans, P. ananatis, and P. allii are the first documented cases of these pathogens of onion in Texas. Identifying and characterizing the nature of onion microflora, including pathogens of onion, is vital to developing rapid disease detection techniques via pathogenomics and minimizing losses through the application of effective disease management measures.

The fungus Colletotrichum orbiculare causes watermelon anthracnose and is an important pathogen of watermelon in the United States, causing a significant impact on yield and quality of the produce. The application of fungicides as preventative and post-occurrence control measures is currently being deployed by growers. Further study of the genetic and molecular basis of anthracnose resistance will help in guiding future watermelon breeding strategies. Several conserved virulence factors (effectors) in C. orbiculare have been reported to interact with the host, at times impairing the host immune machinery. A single dominant gene conferring race 1 anthracnose resistance was reported independently on two watermelon germplasm. The recent advances in genomics, transcriptomics, proteomics, and metabolomics could facilitate a better understanding of the interaction between C. orbiculare effectors and host resistance genes in the already sequenced watermelon genome. In this review, we encompass and discuss (i) the history of watermelon anthracnose, taxonomy, morphology, and diversity in races of C. orbiculare; (ii) the epidemiology of the anthracnose disease and host resistance; (iii) the genetics behind the pathogenesis; and (iv) the current advances in breeding and molecular efforts to elucidate anthracnose resistance.

Bacterial soft rot is an important disease in onion caused by Pectobacterium carotovorum, a Gram-negative bacterium belonging to the Pectobacteriaceae family. The soft rot disease may occur during the preharvest (mature bulbs) or postharvest (transit, storage) stage. We collected symptomatic onion plants from the field and isolated bacteria from the foliage and bulbs. We extracted genomic DNA from the bacterial strain 21TX0081 isolated from onion foliage, conducted a polymerase chain reaction (PCR) based on 16S ribosomal RNA (rRNA)-specific primers, and classified the strain to genus Pectobacterium. To ascertain the species, genome features, and novelty of the strain, we conducted whole genome sequencing and computed average nucleotide identity (ANI) and digital DNA-DNA hybridization (dDDH) values. We also annotated the genome of P. carotovorum strain 21TX0081 using Rapid Annotation using Subsystem Technology (RAST) server. The raw, untrimmed forward and reverse sequence reads of 16S rRNA, and whole genome annotation features have been deposited at Mendeley Data. The datasets generated from consensus 16S rRNA and whole genome sequence have been deposited in National Center for Biotechnology Information (NCBI) repository. They will be useful for future research on comparative genomics and developing tools for disease management in onion.

Pectobacterium brasiliense is a highly destructive bacterial plant pathogen with a broad host range, causing soft rot and blackleg diseases. Genomic resources are for understanding the mechanisms of virulence in these necrotrophic bacteria. In this study, we isolated P. brasiliense strain 25ASUB12 from a symptomatic summer squash fruit growing in a field research plot in Mississippi. This is the first documented case of P. brasiliense in Mississippi. We extracted genomic DNA from the bacterial strain and sequenced it using Oxford Nanopore PromethION and Illumina NovaSeq X Plus platforms to produce a chromosome-level genome sequence of strain 25ASUB12. Genome annotation and comparative genomics were conducted to gain further insights into the strain. Results showed that the genome size of this strain was 4.90 megabases (Mb) and comprises several factors related to pathogenicity such as pectate lyases, diverse secretion factors, siderophores, and quorum-sensing genes. The whole genome of P. brasiliense strain 25ASUB12 serves as a genomic tool to conduct further research on diseases caused by this globally important plant pathogen.