QTL mapping and genomic analyses of earliness and fruit ripening traits in a melon Recombinant Inbred Lines population supported by de novo assembly of their parental genomes.

Earliness and ripening behavior are important attributes of fruits on and off the vine, and affect quality and preference of both growers and consumers. Fruit ripening is a complex physiological process that involves metabolic shifts affecting fruit color, firmness, and aroma production. Melon is a promising model crop for the study of fruit ripening, as the full spectrum of climacteric behavior is represented across the natural variation.

SciApps: An Automated Platform for Processing and Distribution of Plant Genomics Data.

SciApps is an open-source, web-based platform for processing, storing, visualizing, and distributing genomic data and analysis results. Built upon the Tapis (formerly Agave) platform, SciApps brings users TB-scale of data storage via CyVerse Data Store and over one million CPUs via the Extreme Science and Engineering Discovery Environment (XSEDE) resources at Texas Advanced Computing Center (TACC). SciApps provides users ways to chain individual jobs into automated and reproducible workflows in a distributed cloud and provides a management system for data, associated metadata, individual analysis jobs, and multi-step workflows.

SorghumBase: a web-based portal for sorghum genetic information and community advancement.

SorghumBase provides a community portal that integrates genetic, genomic, and breeding resources for sorghum germplasm improvement. Public research and development in agriculture rely on proper data and resource sharing within stakeholder communities. For plant breeders, agronomists, molecular biologists, geneticists, and bioinformaticians, centralizing desirable data into a user-friendly hub for crop systems is essential for successful collaborations and breakthroughs in germplasm development.

A plant cell wall-associated kinase encoding gene is dramatically downregulated during nematode infection of potato.

Plant cell wall associated kinases (WAKs) and WAK-like kinases (WAKLs) have been increasingly recognized as important regulators of plant immunity against various plant pathogens. However, the role of the / family in plant-nematode interactions remains to be determined. Here, we analyzed a -encoding gene () from potato ().

Genomic analyses provide insights into spinach domestication and the genetic basis of agronomic traits.

Spinach is a nutritious leafy vegetable belonging to the family Chenopodiaceae. Here we report a high-quality chromosome-scale reference genome assembly of spinach and genome resequencing of 305 cultivated and wild spinach accessions. Reconstruction of ancestral Chenopodiaceae karyotype indicates substantial genome rearrangements in spinach after its divergence from ancestral Chenopodiaceae, coinciding with high repeat content in the spinach genome.

Multi-year field evaluation of nicotianamine biofortified bread wheat.

Conventional breeding efforts for iron (Fe) and zinc (Zn) biofortification of bread wheat (Triticum aestivum L.) have been hindered by a lack of genetic variation for these traits and a negative correlation between grain Fe and Zn concentrations and yield. We have employed genetic engineering to constitutively express (CE) the rice (Oryza sativa) nicotianamine synthase 2 (OsNAS2) gene and upregulate biosynthesis of two metal chelators - nicotianamine (NA) and 2'-deoxymugineic acid (DMA) - in bread wheat, resulting in increased Fe and Zn concentrations in wholemeal and white flour.

Selection for seed size has uneven effects on specialized metabolite abundance in oat (Avena sativa L.).

Plant breeding strategies to optimize metabolite profiles are necessary to develop health-promoting food crops. In oats (Avena sativa L.), seed metabolites are of interest for their antioxidant properties, yet have not been a direct target of selection in breeding.

Genome-wide association study suggests an independent genetic basis of zinc and cadmium concentrations in fresh sweet corn kernels.

Despite being one of the most consumed vegetables in the United States, the elemental profile of sweet corn (Zea mays L.) is limited in its dietary contributions. To address this through genetic improvement, a genome-wide association study was conducted for the concentrations of 15 elements in fresh kernels of a sweet corn association panel.

Bioexploration and Phylogenetic Placement of Entomopathogenic Fungi of the Genus in Soils of Lebanon Cedar Forests.

The cedar forests of Lebanon have been threatened by the outbreak caused by climate change of a web-spinning sawfly, (Hymenoptera: Pamphiliidae), which negatively impacted the survival of one of the oldest tree species on earth. In this study, we investigated the occurrence of naturally soil-inhabiting entomopathogenic fungi for their role in containing the massive outbreak of this insect. We used a combination of fungal bioexploration methods, including insect bait and selective media.

Interspecific Recombination Between Zucchini Tigre Mosaic Virus and Papaya Ringspot Virus Infecting Cucurbits in China.

Recombination drives evolution of single-stranded RNA viruses and contributes to virus adaptation to new hosts and environmental conditions. Intraspecific recombinants are common in potyviruses, the largest family of single-stranded RNA viruses, whereas interspecific recombinants are rare. Here, we report an interspecific recombination event between papaya ringspot potyvirus (PRSV) and zucchini tigre mosaic potyvirus (ZTMV), two potyviruses infecting cucurbit crops and sharing similar biological characteristics and close phylogenetic relationship.

Ensembl Genomes 2022: an expanding genome resource for non-vertebrates.

Ensembl Genomes (https://www.ensemblgenomes.org) provides access to non-vertebrate genomes and analysis complementing vertebrate resources developed by the Ensembl project (https://www.

Bt Cry1Ac resistance in Trichoplusia ni is conferred by multi-gene mutations.

The three-domain Cry toxin Cry1Ac from Bacillus thuringiensis （Bt） is an important insecticidal toxin in Bt sprays and has been used in transgenic Bt-crops to confer insect resistance. The cabbage looper, Trichoplusia ni, has developed resistance to Bt sprays in commercial greenhouses, and the resistance to Cry1Ac has been previously identified to be associated with altered expression of the APN1 and APN6 genes and be genetically linked to a locus on chromosome 15. In this study, the Cry1Ac resistance locus in T.

A systems genetics approach reveals PbrNSC as a regulator of lignin and cellulose biosynthesis in stone cells of pear fruit.

Background: Stone cells in fruits of pear (Pyrus pyrifolia) negatively influence fruit quality because their lignified cell walls impart a coarse and granular texture to the fruit flesh.

Results: We generate RNA-seq data from the developing fruits of 206 pear cultivars with a wide range of stone cell contents and use a systems genetics approach to integrate co-expression networks and expression quantitative trait loci (eQTLs) to characterize the regulatory mechanisms controlling lignocellulose formation in the stone cells of pear fruits. Our data with a total of 35,897 expressed genes and 974,404 SNPs support the identification of seven stone cell formation modules and the detection of 139,515 eQTLs for 3229 genes in these modules.

The roles of selectivity filters in determining aluminum transport by AtNIP1;2.

Aquaporins (AQPs) are channel proteins involved in transporting a variety of substrates. It has been proposed that the constriction regions in the central pores of the AQP channels play a crucial role in determining transport substrates and activities of AQPs. Our previous results suggest that AtNIP1;2, a member of the AQP superfamily in Arabidopsis, facilitates aluminum transport across the plasma membrane.

Identification of Indole-3-Acetic Acid-Regulated Genes in pv. tomato Strain DC3000.

The auxin indole-3-acetic acid (IAA) is a plant hormone that not only regulates plant growth and development but also plays important roles in plant-microbe interactions. We previously reported that IAA alters expression of several virulence-related genes in the plant pathogen Pseudomonas syringae pv. tomato strain DC3000 (DC3000).

Tad pilus-mediated twitching motility is essential for DNA uptake and survival of Liberibacters.

Axenically cultured Liberibacter crescens (Lcr) is a closely related surrogate for uncultured plant pathogenic species of the genus Liberibacter, including 'Candidatus L. asiaticus' (CLas) and 'Ca. L.

Multi-omics prediction of oat agronomic and seed nutritional traits across environments and in distantly related populations.

Integration of multi-omics data improved prediction accuracies of oat agronomic and seed nutritional traits in multi-environment trials and distantly related populations in addition to the single-environment prediction. Multi-omics prediction has been shown to be superior to genomic prediction with genome-wide DNA-based genetic markers (G) for predicting phenotypes. However, most of the existing studies were based on historical datasets from one environment; therefore, they were unable to evaluate the efficiency of multi-omics prediction in multi-environment trials and distantly related populations.

Strongwellsea crypta (Entomophthorales: Entomophthoraceae), a new species infecting Botanophila fugax (Diptera: Anthomyiidae).

A new species from the genus Strongwellsea (Entomophthorales: Entomophthoraceae) is described: Strongwellsea crypta Eilenberg & Humber from adult Botanophila fugax (Meigen) (Diptera: Anthomyiidae). The description is based on pathobiological, phenotypical and genotypical characters. The abdominal holes in infected hosts develop rapidly and become strikingly large and edgy, almost rhomboid in shape.

Genome-wide association study reveals the genetic architecture of 27 agronomic traits in tomato.

Tomato (Solanum lycopersicum) is a highly valuable fruit crop, and yield is one of the most important agronomic traits. However, the genetic architecture underlying tomato yield-related traits has not been fully addressed. Based on ∼4.

Overexpression of native ORANGE (OR) and OR mutant protein in Chlamydomonas reinhardtii enhances carotenoid and ABA accumulation and increases resistance to abiotic stress.

The carotenoid content of plants can be increased by overexpression of the regulatory protein ORANGE (OR) or a mutant variant known as the 'golden SNP'. In the present study, a strong light-inducible promoter was used to overexpress either wild type CrOR (CrOR) or a mutated CrOR (CrOR) containing a single histidine substitution for a conserved arginine in the microalgae Chlamydomonas reinhardtii. Overexpression of CrOR and CrOR roughly doubled and tripled, respectively, the accumulation of several different carotenoids, including β-carotene, α-carotene, lutein and violaxanthin in C.

Genetic characterization of melon accessions in the U.S. National Plant Germplasm System and construction of a melon core collection.

Melon (C. melo L.) is an economically important vegetable crop cultivated worldwide.